##### Table of Contents





UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549





FORM 10-Q







|x | QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ---------------------------------------------------------------------------------------

For the quarterly period ended June 30, 2010

OR



| ̈ | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ----------------------------------------------------------------------------------------

For the transition period from  to

Commission File Number 001-33095





ACHILLION PHARMACEUTICALS, INC.

(Exact name of registrant as specified in its charter)







|                                                               |  |                                     
|-------------------------------------------------------------- |  | ------------------------------------
|Delaware                                                       |  | 52-2113479                          
|(State or other jurisdiction of
incorporation or organization) |  | (I.R.S. Employer
Identification No.)
|                                                               | 
|300 George Street, New Haven, CT                               |  | 06511                               
|(Address of principal executive offices)                       |  | (Zip Code)                          

(203)
624-7000

(Registrants telephone number, including area code)





Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the
Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90
days.    Yes  x    No   ̈

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate website, if any, every Interactive
Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such
files).    Yes   ̈    No   ̈

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, non-accelerated filer or a smaller
reporting company. See definition of accelerated filer, large accelerated filer and smaller reporting company in Rule 12b-2 of the Exchange Act. (Check one):



|                        |  |                                                |  |                           |  |  
|----------------------- |  | ---------------------------------------------- |  | ------------------------- |  | -
|Large accelerated filer |  |  ̈                                              |  | Accelerated filer         |  |  ̈
|                        |  |                                                | 
|Non-accelerated filer   |  |  ̈  (Do not check if smaller reporting company) |  | Smaller reporting company |  | x

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange
Act).    Yes   ̈    No  x

As of August 12, 2010, the registrant had 38,548,327 shares of Common Stock, $0.001 par value per share, outstanding.









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INDEX



|                              |  |                                                                                                |  |           
|----------------------------- |  | ---------------------------------------------------------------------------------------------- |  | ----------
|                              |  |                                                                                                |  | PAGENUMBER
|PART I. FINANCIAL INFORMATION |  |                                                                                               
|                              |  |                                                                                               
|ITEM 1.                       |  | FINANCIAL STATEMENTS                                                                           |  |           
|                              |  |                                                                                               
|                              |  | Balance Sheets at June 30, 2010 and December 31, 2009 (unaudited)                              |  | 3         
|                              |  | Statements of Operations for the three and six months ended June 30, 2010 and 2009
(unaudited) |  | 4         
|                              |  | Statements of Cash Flows for the six months ended June 30, 2010 and 2009
(unaudited)           |  | 5         
|                              |  | Notes to Financial Statements (unaudited)                                                      |  | 6         
|                              |  |                                                                                               
|ITEM 2.                       |  | MANAGEMENTS DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF
OPERATIONS          |  | 14        
|                              |  |                                                                                               
|ITEM 3.                       |  | QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK                                     |  | 24        
|                              |  |                                                                                               
|ITEM 4.                       |  | CONTROLS AND PROCEDURES                                                                        |  | 24        
|                              | 
|PART II. OTHER INFORMATION    |  |                                                                                               
|                              |  |                                                                                               
|ITEM 1A.                      |  | RISK FACTORS                                                                                   |  | 25        
|                              |  |                                                                                               
|ITEM 6.                       |  | EXHIBITS                                                                                       |  | 40        



2



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PART I. FINANCIAL INFORMATION



|ITEM 1. | FINANCIAL STATEMENTS
|------- | --------------------

Achillion Pharmaceuticals, Inc.

Balance Sheets

(in thousands, except per share data)

(Unaudited)



|                                                                                                                                                               |  |               |          |   |                   |   |          |  
|-------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | ------------- | -------- | - | ----------------- | - | -------- | -
|                                                                                                                                                               |  | June 30, 2010 |          |   | December 31, 2009 |  
|Assets                                                                                                                                                         |  |               |          |   |                   |   |          |  
|Current assets:                                                                                                                                                |  |               |          |   |                   |   |          |  
|Cash and cash equivalents                                                                                                                                      |  | $             | 14,228   |   |                   | $ | 9,712    |  
|Marketable securities                                                                                                                                          |  |               | 5,271    |   |                   |   |         |  
|Accounts receivable                                                                                                                                            |  |               | 187      |   |                   |   | 65       |  
|Prepaid expenses and other current assets                                                                                                                      |  |               | 1,144    |   |                   |   | 768      |  
|                                                                                                                                                               |  |               |          |   |                   |   |          |  
|Total current assets                                                                                                                                           |  |               | 20,830   |   |                   |   | 10,545   |  
|Fixed assets, net                                                                                                                                              |  |               | 678      |   |                   |   | 876      |  
|Deferred financing costs                                                                                                                                       |  |               | 133      |   |                   |   | 149      |  
|Restricted cash                                                                                                                                                |  |               | 152      |   |                   |   | 100      |  
|                                                                                                                                                               |  |               |          |   |                   |   |          |  
|Total assets                                                                                                                                                   |  | $             | 21,793   |   |                   | $ | 11,670   |  
|                                                                                                                                                               |  |               |          |   |                   |   |          |  
|Liabilities and Stockholders Equity                                                                                                                           |  |               |          |   |                   |   |          |  
|Current liabilities:                                                                                                                                           |  |               |          |   |                   |   |          |  
|Accounts payable                                                                                                                                               |  | $             | 2,345    |   |                   | $ | 2,277    |  
|Accrued expenses                                                                                                                                               |  |               | 2,185    |   |                   |   | 2,598    |  
|Current portion of long-term debt                                                                                                                              |  |               | 2,162    |   |                   |   | 2,867    |  
|                                                                                                                                                               |  |               |          |   |                   |   |          |  
|Total current liabilities                                                                                                                                      |  |               | 6,692    |   |                   |   | 7,742    |  
|Deferred revenue                                                                                                                                               |  |               | 2,489    |   |                   |   | 2,489    |  
|Long term debt                                                                                                                                                 |  |               |         |   |                   |   | 417      |  
|                                                                                                                                                               |  |               |          |   |                   |   |          |  
|Total liabilities                                                                                                                                              |  |               | 9,181    |   |                   |   | 10,648   |  
|                                                                                                                                                               |  |               |          |   |                   |   |          |  
|Commitments and contingencies                                                                                                                                  |  |               |          |   |                   |   |          |  
|Stockholders Equity:                                                                                                                                          |  |               |          |   |                   |   |          |  
|Common Stock, $.001 par value; 100,000 shares authorized: 38,548 and 26,706 shares issued and outstanding at June 30, 2010
and December 31, 2009, respectively |  |               | 39       |   |                   |   | 27       |  
|Additional paid-in capital                                                                                                                                     |  |               | 230,512  |   |                   |   | 206,908  |  
|Accumulated deficit                                                                                                                                            |  |               | (217,933 | ) |                   |   | (205,913 | )
|Accumulated other comprehensive income                                                                                                                         |  |               | (6       | ) |                   |   |         |  
|                                                                                                                                                               |  |               |          |   |                   |   |          |  
|Total stockholders equity                                                                                                                                     |  |               | 12,612   |   |                   |   | 1,022    |  
|                                                                                                                                                               |  |               |          |   |                   |   |          |  
|Total liabilities and stockholders equity                                                                                                                     |  | $             | 21,793   |   |                   | $ | 11,670   |  
|                                                                                                                                                               |  |               |          |   |                   |   |          |  

The accompanying notes are an integral part of these (unaudited) financial statements.



3



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Achillion Pharmaceuticals, Inc.

Statements of Operations

(in thousands, except per share amounts)

(Unaudited)



|                                                                               |  |                                     |        |   |                                   |   |        |      |  |   |         |   |  |   |         |  
|------------------------------------------------------------------------------ |  | ----------------------------------- | ------ | - | --------------------------------- | - | ------ | ---- |  | - | ------- | - |  | - | ------- | -
|                                                                               |  | For the Three Months Ended June 30, |        |   | For the Six Months Ended June 30, |  
|                                                                               |  | 2010                                |        |   | 2009                              |   |        | 2010 |  |   | 2009    |  
|Revenue                                                                        |  | $                                   | 187    |   |                                   | $ | (7     | )    |  | $ | 261     |   |  | $ | (300    | )
|                                                                               |  |                                     |        |   |                                   |   |        |      |  |   |         |   |  |   |         |  
|Operating expenses                                                             |  |                                     |        |   |                                   |   |        |      |  |   |         |   |  |   |         |  
|Research and development                                                       |  |                                     | 4,814  |   |                                   |   | 4,399  |      |  |   | 8,773   |   |  |   | 9,136   |  
|General and administrative                                                     |  |                                     | 1,690  |   |                                   |   | 1,598  |      |  |   | 3,357   |   |  |   | 3,201   |  
|                                                                               |  |                                     |        |   |                                   |   |        |      |  |   |         |   |  |   |         |  
|Total operating expenses                                                       |  |                                     | 6,504  |   |                                   |   | 5,997  |      |  |   | 12,130  |   |  |   | 12,337  |  
|                                                                               |  |                                     |        |   |                                   |   |        |      |  |   |         |   |  |   |         |  
|Loss from operations                                                           |  |                                     | (6,317 | ) |                                   |   | (6,004 | )    |  |   | (11,869 | ) |  |   | (12,637 | )
|                                                                               |  |                                     |        |   |                                   |   |        |      |  |   |         |   |  |   |         |  
|Other income (expense)                                                         |  |                                     |        |   |                                   |   |        |      |  |   |         |   |  |   |         |  
|Interest income                                                                |  |                                     | 15     |   |                                   |   | 57     |      |  |   | 25      |   |  |   | 149     |  
|Interest expense                                                               |  |                                     | (82    | ) |                                   |   | (144   | )    |  |   | (176    | ) |  |   | (327    | )
|                                                                               |  |                                     |        |   |                                   |   |        |      |  |   |         |   |  |   |         |  
|Net loss                                                                       |  |                                     | (6,384 | ) |                                   |   | (6,091 | )    |  |   | (12,020 | ) |  |   | (12,815 | )
|                                                                               |  |                                     |        |   |                                   |   |        |      |  |   |         |   |  |   |         |  
|Basic and diluted net loss per share (Note 5)                                  |  | $                                   | (0.17  | ) |                                   | $ | (0.23  | )    |  | $ | (0.32   | ) |  | $ | (0.48   | )
|                                                                               |  |                                     |        |   |                                   |   |        |      |  |   |         |   |  |   |         |  
|Weighted average shares used in computing basic and diluted net loss per share |  |                                     | 38,540 |   |                                   |   | 26,419 |      |  |   | 37,066  |   |  |   | 26,409  |  
|                                                                               |  |                                     |        |   |                                   |   |        |      |  |   |         |   |  |   |         |  

The accompanying notes are an integral part of these (unaudited) financial statements.



4



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Achillion Pharmaceuticals, Inc.

Statements of Cash Flows

(in thousands)

(Unaudited)



|                                                                            |  |                           |         |   |      |   |         |  
|--------------------------------------------------------------------------- |  | ------------------------- | ------- | - | ---- | - | ------- | -
|                                                                            |  | Six Months Ended June 30, |        
|                                                                            |  | 2010                      |         |   | 2009 |  
|Cash flows from operating activities                                        |  |                           |         |   |      |   |         |  
|Net loss                                                                    |  | $                         | (12,020 | ) |      | $ | (12,815 | )
|Adjustments to reconcile net loss to net cash used in operating activities: |  |                           |         |   |      |   |         |  
|Depreciation and amortization                                               |  |                           | 372     |   |      |   | 410     |  
|Noncash stock-based compensation                                            |  |                           | 938     |   |      |   | 976     |  
|Noncash interest expense                                                    |  |                           | 26      |   |      |   | 45      |  
|Loss on disposal of equipment                                               |  |                           | 4       |   |      |   |        |  
|Amortization of premium on marketable securities                            |  |                           | 88      |   |      |   | 100     |  
|Changes in operating assets and liabilities:                                |  |                           |         |   |      |   |         |  
|Accounts receivable                                                         |  |                           | (122    | ) |      |   |        |  
|Prepaid expenses and other current assets                                   |  |                           | (435    | ) |      |   | 84      |  
|Accounts payable                                                            |  |                           | 68      |   |      |   | (1,237  | )
|Accrued expenses                                                            |  |                           | (413    | ) |      |   | (255    | )
|                                                                            |  |                           |         |   |      |   |         |  
|Net cash used in operating activities                                       |  |                           | (11,494 | ) |      |   | (12,692 | )
|                                                                            |  |                           |         |   |      |   |         |  
|Cash flows from investing activities                                        |  |                           |         |   |      |   |         |  
|Purchase of property and equipment                                          |  |                           | (155    | ) |      |   | (42     | )
|Purchase of available for sale marketable securities                        |  |                           | (5,665  | ) |      |   | (5,680  | )
|Maturities of marketable securities                                         |  |                           | 300     |   |      |   | 18,590  |  
|                                                                            |  |                           |         |   |      |   |         |  
|Net cash (used in) provided by investing activities                         |  |                           | (5,520  | ) |      |   | 12,868  |  
|                                                                            |  |                           |         |   |      |   |         |  
|Cash flows from financing activities                                        |  |                           |         |   |      |   |         |  
|Proceeds from sale of common stock, net of issuance costs                   |  |                           | 22,628  |   |      |   |        |  
|Proceeds from sale of common stock under the Employee Stock Purchase Plan   |  |                           | 50      |   |      |   | 55      |  
|Repayments of debt payable                                                  |  |                           | (1,148  | ) |      |   | (1,905  | )
|                                                                            |  |                           |         |   |      |   |         |  
|Net cash provided by (used in) financing activities                         |  |                           | 21,530  |   |      |   | (1,850  | )
|                                                                            |  |                           |         |   |      |   |         |  
|Net increase (decrease) in cash and cash equivalents                        |  |                           | 4,516   |   |      |   | (1,674  | )
|Cash and cash equivalents, beginning of period                              |  |                           | 9,712   |   |      |   | 11,060  |  
|                                                                            |  |                           |         |   |      |   |         |  
|Cash and cash equivalents, end of period                                    |  | $                         | 14,228  |   |      | $ | 9,386   |  
|                                                                            |  |                           |         |   |      |   |         |  
|Supplemental disclosure of cash flow information                            |  |                           |         |   |      |   |         |  
|Cash paid for interest                                                      |  | $                         | 138     |   |      | $ | 274     |  

The accompanying notes
are an integral part of these (unaudited) financial statements.



5



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Achillion Pharmaceuticals, Inc.

Notes to Financial Statements

(in thousands, except per share amounts)

(Unaudited)

1. Nature
of the Business

Achillion Pharmaceuticals, Inc. (the Company) was incorporated on August 17, 1998 in
Delaware. The Company was established to discover, develop and commercialize innovative anti-infective drug therapies. The Company is devoting substantially all of its efforts towards product research and development.

The Company incurred losses of $204,071 from inception through June 30, 2010. The Company has funded its operations primarily
through the sale of equity securities, borrowings from debt facilities and the receipt of milestone and cost-sharing receipts from its collaboration partner, Gilead Sciences, Inc. (Gilead).

The Company believes that its existing cash, cash equivalents and marketable securities, as potentially augmented by its Standby Equity
Distribution Agreement (SEDA), with YA Global Master SPV Ltd. (YA Global) (see Note 4) or additional financing activities, will be sufficient to support its current operating plan through at least June 30, 2011.
However, the Companys operating plan may change as a result of many factors, including:



| |  |  | the costs involved in the clinical development, manufacturing and formulation of ACH-1625;
| | - |  | ------------------------------------------------------------------------------------------



| |  |  | the costs associated with the investigational new drug (IND) application preparation, including the required chemical manufacturing and
control (CMC) work, related to ACH-1095;
| | - |  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | the costs associated with the preclinical development and manufacturing of ACH-2684 and ACH-2928;
| | - |  | -------------------------------------------------------------------------------------------------



| |  |  | the partnership opportunities for ACH-702 that the Company may pursue;
| | - |  | ----------------------------------------------------------------------



| |  |  | the Companys ability to enter into corporate collaborations and the terms and success of these collaborations; and
| | - |  | -------------------------------------------------------------------------------------------------------------------



| |  |  | the Companys ability to raise incremental debt or equity capital, including any changes in the credit market that may impact its ability to
obtain capital in the future.
| | - |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------

In January 2010, the Company issued 10,275 shares of its common stock in
an underwritten public offering. In February 2010, the Company issued an additional 1,541 shares of common stock in connection with the underwriters exercise of an over-allotment option. The Company received net proceeds of $22,628.

The Company expects to incur substantial and increasing losses for at least the next several years and will need substantial
additional financing to obtain regulatory approvals, fund operating losses, and, if deemed appropriate, establish manufacturing and sales and marketing capabilities, which the Company may seek to raise through public or private equity or debt
financings, collaborative or other arrangements with third parties or through other sources of financing. There can be no assurance that such funding will be available on terms favorable to the Company, if at all.

In addition to the normal risks associated with early-stage companies, there can be no assurance that the Company will successfully
complete its research and development, obtain adequate patent protection for its technology, obtain necessary government regulatory approval for drug candidates the Company develops, find and maintain partners for certain drug candidates or that any
approved drug candidates will be commercially viable. In addition, the Company may not be profitable even if it succeeds in commercializing any of its drug candidates.

Certain prior period amounts have been reclassified to conform to the current years presentation. State research and development
credit carryforwards that were exchanged for cash of $30 and $70 were reclassified from income tax benefit to a reduction of research and development expenditures for the three and six months ended June 30, 2009, respectively.

2. Accounting Standards Updates

In October 2009, an update was made to ASC 605, Revenue Recognition,which provides accounting principles and application guidance
on how revenue arrangements with multiple deliverables should be separated and the consideration allocated. This guidance eliminates the requirement to establish the fair value of undelivered products and services for separate revenue recognition.
Allocation of consideration is now based on managements estimate of the selling price for an undelivered item where



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Achillion Pharmaceuticals, Inc.

Notes to Financial Statements(Continued)

(in thousands, except per share amounts)

(Unaudited)



there is no other means to determine the fair value of that undelivered item. This update is effective prospectively for revenue arrangements entered into or materially modified in fiscal years
beginning on or after June 15, 2010. Early adoption of this update is permitted; however, the Company will be required to apply the provisions of the amendment retrospectively to the beginning of its fiscal year. The Company is currently
evaluating the potential impact of this standard on its financial position and results of operations.

In January 2010, the
Financial Accounting Standards Board (FASB) issued Accounting Standards Update (ASU) 2010-06 which amended guidance on fair value measurement and disclosures. The new guidance requires additional disclosures regarding fair
value measurements and provides clarification regarding the level of disaggregation of fair value disclosures by investment class. This guidance is effective for reporting periods beginning after December 15, 2009 except for the additional
level 3 requirements which is effective for reporting periods beginning after December 15, 2010. There was no impact to the Companys financial statements upon adoption.

In April 2010, the FASB issued Accounting Standard Update No. 2010-17,Milestone Method of Revenue Recognition, which
provides guidance on applying the milestone method to milestone payments for achieving specified performance measures when those payments are related to uncertain future events. However, the FASB clarified that, even if the requirements in this ASU
are met, entities would not be precluded from making an accounting policy election to apply another appropriate accounting policy that results in the deferral of some portion of the arrangement consideration. The ASU is effective for periods
beginning on or after June 15, 2010. Early application was permitted. Entities can apply this guidance retrospectively as well as prospectively to milestones achieved after adoption. There was no impact to the Companys financial
statements upon adoption.

3. Basis of Presentation

The accompanying unaudited financial statements of the Company should be read in conjunction with the audited financial statements and
notes as of and for the year ended December 31, 2009 included in the Companys Annual Report on Form 10-K filed with the SEC on March 11, 2010. The accompanying unaudited financial statements have been prepared in accordance with
generally accepted accounting principles in the United States (U.S. GAAP) for interim financial information, in accordance with the instructions to Form 10-Q and the guidance in Article 10 of Regulation S-X. Accordingly, since
they are interim financial statements, the accompanying unaudited financial statements do not include all of the information and disclosures required by U.S. GAAP for complete financial statements. The accompanying financial statements reflect all
adjustments, consisting of normal recurring adjustments, that are, in the opinion of management, necessary for a fair statement of the results of operations for the interim periods presented. Interim results are not necessarily indicative of results
for a full year.

The preparation of financial statements in accordance with U.S. GAAP requires management to make estimates
and assumptions that affect amounts reported in the financial statements and notes thereto. A discussion of the Companys critical accounting policies and management estimates is described in Managements Discussion and Analysis of
Financial Condition and Results of Operations included in Part I, Item II of this quarterly report on Form 10-Q.

4. Financing
Activities

Public Offering

On January 22, 2010, the Company entered into an underwriting agreement (the Underwriting Agreement) with Roth Capital
Partners, LLC, Noble Financial Capital Markets and National Securities Corporation, as underwriters (the Underwriters), related to a public offering of shares of the Companys common stock, par value $.001 per share, at a price of
$2.08 per share less underwriting discounts and commissions (the Offering). The Company issued and sold 10,275 shares of common stock in connection with the Offering on January 27, 2010.

On February 2, 2010, the Company issued and sold an additional 1,541 shares of common stock in connection with the exercise of the
over-allotment option that was granted to the underwriters in the Underwriting Agreement.

The Offering resulted in net
proceeds to the Company of $22,628. The Company intends to use the net proceeds for general corporate purposes, research and development expenses, including clinical trial costs, general and administrative expenses and products and technologies that
complement its business. The Company has invested the net proceeds in investment-grade, interest bearing securities.



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##### Table of Contents

Achillion Pharmaceuticals, Inc.

Notes to Financial Statements(Continued)

(in thousands, except per share amounts)

(Unaudited)



Standby Equity Distribution Agreement (SEDA)

On July 1, 2009, the Company entered into a SEDA with YA Global pursuant to which the Company may, at its sole and exclusive option,
periodically sell to YA Global shares of its common stock, $0.001 par value per share, for total proceeds of up to $15,000. Each advance under the SEDA shall not exceed the greater of $300 or the average daily trading volume of the Companys
common stock for the five consecutive trading days prior to the notice date. Advance notices may be given to YA Global once every five trading days. For each share of common stock purchased pursuant to an advance under the SEDA, YA Global will pay
to the Company ninety-five percent of the lowest volume-weighted average price of the common stock on the NASDAQ Global Market during the five consecutive trading days following delivery by the Company of an advance notice. Additionally, in no event
shall the number of shares of common stock issued under the SEDA cause YA Global to own more than 9.99% of the Companys common stock as of July 1, 2009 (5,292 shares), unless the Company obtains stockholder approval or obtains a written
opinion from counsel that such approval is not required. The Company is not obligated to utilize any of the $15,000 available under the SEDA and there are no minimum commitments or minimum use penalties. The Company issued YA Global 191 shares of
its common stock as a commitment fee in connection with the transaction and also paid a due diligence and structuring fee of $25. These shares of common stock, as well as any additional shares of common stock the Company may issue pursuant to the
SEDA in the future, have been registered on a registration statement that was declared effective on September 21, 2009. The SEDA has two year term and may be terminated by the Company at any time. The Company capitalized $105 of issuance costs
related to the SEDA. As of June 30, 2010, there were no advances under the SEDA.

5. Earnings (Loss) Per Share (EPS)

Basic EPS is calculated by dividing net income or loss attributable to common stockholders by the weighted average common
stock outstanding. Diluted EPS is calculated by adjusting weighted average common shares outstanding for the dilutive effect of common stock options and warrants. In periods in which a net loss is recorded, no effect is given to potentially dilutive
securities, since the effect would be antidilutive. Securities that could potentially dilute basic EPS in the future were not included in the computation of diluted EPS because to do so would have been antidilutive. Potentially dilutive securities
were as follows for the three and six months ended June 30, 2010 and 2009 (prior to consideration of the treasury stock method):



|                                                  |  |                                     |  |      
|------------------------------------------------- |  | ----------------------------------- |  | -----
|                                                  |  | Three and Six Months Ended June 30,
|                                                  |  | 2010                                |  | 2009 
|Options                                           |  | 3,336                               |  | 2,713
|Warrants                                          |  | 2,785                               |  | 6,711
|                                                  |  |                                     |  |      
|Total potentially dilutive securities outstanding |  | 6,121                               |  | 9,424
|                                                  |  |                                     |  |      

In August 2009, 3,679 warrants issued in connection
with the Companys private placement financing in August 2008 expired unexercised.

6. Collaboration Arrangement

Gilead Sciences, Inc.

In November 2004, the Company entered into a research collaboration and license agreement with Gilead Sciences, Inc. pursuant to which the
Company agreed to collaborate exclusively with Gilead throughout the world to develop and commercialize compounds for the treatment of chronic hepatitis C and which inhibit HCV replication through a novel mechanism of action targeting the HCV NS4A
protein. In May 2009, Gilead informed the Company that they did not intend to pursue development of its lead compound ACH-1095. The Company believes the compound should be advanced and therefore in September 2009, the Company and Gilead amended the
collaboration arrangement so that the Company may continue to develop ACH-1095 independently during an Interim Period, while Gilead may rejoin in the development of ACH-1095 at clinical proof-of-concept, as defined. The Company will bear
all costs associated with ACH-1095 development during this Interim Period. If Gilead elects to regain rights to ACH-1095, Gilead will reimburse the Company for all ACH-1095 development costs incurred during the Interim Period, and all original
milestone and royalty payments described in the license agreement will again apply to ACH-1095. Gilead is under no obligation to exercise any rights with respect to ACH-1095. If Gilead elects not to exercise its rights to ACH-1095 within forty-five
(45) days after proof-of-concept, the Company shall gain all rights to ACH-1095, and Gilead will then have the right to designate a new lead compound under the license agreement.



8



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##### Table of Contents

Achillion Pharmaceuticals, Inc.

Notes to Financial Statements(Continued)

(in thousands, except per share amounts)

(Unaudited)



Regardless of Gileads election to exercise its rights with respect to ACH-1095,
during the Interim Period the parties retain their rights to compounds which were identified under the collaboration prior to the effective date of the Amendment. The terms of the original License Agreement, including milestone, royalty and
cost-sharing provisions, shall apply to the development of such other compounds. New lead compounds under the collaboration can be identified by mutual agreement of the parties.

Gilead has the right to terminate the agreement without cause upon 30 days written notice to the Company. Upon termination of the Gilead
Arrangement for any reason, all cost share amounts due and payable through the date of termination shall be paid by the appropriate party and no previously paid amounts will be refundable. In addition to Gileads rights to unilaterally
terminate this agreement, each party has the right to terminate for material breach; however, the Company may terminate for Gileads breach only on a market-by-market basis, and, if applicable, a product-by-product basis.

If Gilead elects to exercise its rights with respect to development of ACH-1095 or if the Company and Gilead pursue a back-up compound,
research and development activities prior to proof-of-concept will be overseen by a research committee comprised of equal numbers of the Companys representatives and representatives from Gilead. The joint research committee assigns research
and development tasks, agrees upon a budget for the research program, and shares equally in the related costs. In addition, the parties may agree at any time to increase or decrease the research budget. Prior to proof-of-concept, any disputes within
the joint research committee that cannot be resolved between designated executives of each party will be resolved by Gilead.

The Company continues to be responsible for back-up activities, which includes preclinical assessment of a limited number of other NS4A
antagonists until such time as proof-of-concept is achieved. Gilead will otherwise be responsible for all manufacturing, formulation and commercialization activities associated with such compounds, if nominated, including all regulatory filings and
clinical trials after proof-of-concept unless Gilead chooses not to opt back in on ACH-1095 development. Gilead has agreed under the agreement to use reasonably diligent efforts to develop and commercialize at least one compound in each of the
United States, Japan, Germany, France, Italy, Spain and the United Kingdom.

The Company received $10,000 from Gilead upon the
execution of the license agreement, consisting of license fees and an equity investment, and could receive up to $157,500 in development, regulatory and sales milestone payments, assuming the successful simultaneous development of a lead and back-up
compound, and annual sales in excess of $600,000. The Company may also receive royalties on net sales of products if commercialization is achieved.

The up-front payment of $10,000, received in 2004, was first allocated to the fair value of the Series C-1, in which each share of the
Series C-1 was determined to be worth $0.88 per share, or approximately $2,000 in aggregate. The remaining $8,000 balance of the $10,000 is being accounted for as a non-refundable up-front license fee. Due to certain provisions contained within the
Gilead Arrangement relating to services to be performed on both the primary and back-up compounds, as defined in the Gilead Arrangement, the non-refundable up-front license fee of $8,000, as well as a $2,000 milestone achieved during the period
prior to achievement of proof-of-concept (the Research Period), is being accounted for under the proportionate performance model. Future milestones, if any, will occur after the Research Period, are not accounted for under the
proportionate performance model and will be recognized when the milestone is achieved as the Company has no further research or development obligations after the Research Period.

Under collaboration arrangements, payments received during the period of performance generally include up-front payments, time-or
performance-based milestones and reimbursement of internal and external costs. The proportion of actual performance to total expected performance is applied to these payments in determining periodic revenue. Revenue recognized will be limited by the
aggregate cash received or receivable to date by the Company.

In the first quarter of 2009, the Company and Gilead revised
their joint research program to increase total estimated efforts under the collaboration and extended the estimated period over which the Companys remaining obligations under the arrangement would be completed. At this time, the Company cannot
accurately estimate its future obligations under the collaboration as it has not identified a new lead compound that will be developed jointly. Therefore, during the six months ended June 30, 2010 and 2009, the Company did not recognize revenue
from upfront, milestone and full-time equivalent, or FTE fees previously received under the collaboration. The Company will determine its remaining obligations if and when a new lead compound is identified.

During the three months ended June 30, 2010 and 2009, the Company recognized revenue of $43 and $(7), respectively, under the Gilead
Arrangement, all of which related to external costs billed by the Company to Gilead, net of Gilead billings to the Company of $0 and $66 for the three months ended June 30, 2010 and 2009, respectively. Payments to Gilead under this
collaboration are recognized as a reduction in revenue. Recognition of external costs incurred by Gilead exceeded amounts recognized under the proportionate performance model, resulting in negative revenue for the three months ended June 30,
2009.



9



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##### Table of Contents

Achillion Pharmaceuticals, Inc.

Notes to Financial Statements(Continued)

(in thousands, except per share amounts)

(Unaudited)



During the six months ended June 30, 2010 and 2009, the Company recognized revenue
of $117 and $(300), respectively, under the Gilead Arrangement, all of which related to external costs billed by the Company to Gilead, net of Gilead billings to the Company of $0 and $428 for the six months ended June 30, 2010 and 2009,
respectively. Payments to Gilead under this collaboration are recognized as a reduction in revenue. Recognition of external costs incurred by Gilead exceeded amounts recognized under the proportionate performance model, resulting in negative revenue
for the six months ended June 30, 2009.

Included in the accompanying balance sheets as of June 30, 2010 and
December 31, 2009 are $43 and $61 respectively, of accounts receivable resulting from this collaboration agreement and $2,489 and $2,489, respectively, of deferred revenue resulting from the up-front fee, a milestone payment, and FTE costs.

GCA Therapeutics, Ltd.

On February 1, 2010, the Company entered into a license agreement (the Agreement) with GCA Therapeutics, Ltd.
(GCAT) for elvucitabine, the Companys nucleoside reverse transcriptase inhibitor for the treatment of both hepatitis B virus (HBV) infection and human immunodeficiency virus (HIV) infection. The Agreement
was amended and restated on March 8, 2010. The exclusive license grants GCAT the right, through a Chinese joint venture with Tianjing Institute of Pharmaceutical Research, to clinically develop and commercialize elvucitabine in mainland China,
Hong Kong and Taiwan.

Under the terms of the Agreement, GCAT, through a sublicense agreement with a Chinese joint venture,
T&T Pharma Co., Ltd., will assume all development and regulatory responsibility and associated costs for elvucitabine. There was no financial impact upon the signing of the agreement. The Company will be eligible to receive development
milestones and royalties on net sales in those territories.

The Agreement may be terminated by either party based upon
material breaches by the other party, effective 90 days after providing written notice to the breaching party, if the breaching party fails to cure its material breach.

The Company may terminate the Agreement upon 30 days written notice in the event GCAT fails to meet any of the development or
commercialization diligence milestones by the deadlines specified in the Agreement, or may terminate upon 90 days written notice in the event of a change of corporate control. In the event of a change of control, as defined, the Company shall pay
GCAT termination fees, in an amount determined based upon specified progress milestones.

7. Marketable Securities

The Company applies the provisions of ASC 820, Fair Value Measurements and Disclosures, for financial assets and liabilities
measured on a recurring basis which requires disclosure that establishes a framework for measuring fair value and expands disclosures in the financial statements. The statement requires that fair value measurements be classified and disclosed in one
of the three categories:

Level 1: Quoted prices in active markets for identical assets and liabilities that the reporting
entity has the ability to access at the measurement date;

Level 2: Inputs other than quoted prices included within Level 1
that are observable for the asset or liability, either directly or indirectly; or

Level 3: Unobservable inputs.

The fair value of the Companys securities of $5,271 and $0 as of June 30, 2010 and December 31, 2009, respectively, is
valued based on level 2 inputs. The Companys investments consist mainly of U.S government and agency securities, government sponsored bond obligations and certain other corporate debt securities. Fair value is determined based upon quoted
market prices; however, due to lack of sufficiency of transactions and trading volume, the Company has assessed these as level 2 within the fair value hierarchy of ASC 820. The Company classifies its entire investment portfolio as available for sale
as defined in ASC 320, Debt and Equity Securities. The maturities of all marketable securities held at June 30, 2010 are less than one year. Securities are carried at fair value with the unrealized gains (losses) reported as a separate
component of stockholders equity.

The unrealized gain (loss) from marketable securities was $(6) and $0 at
June 30, 2010 and December 31, 2009, respectively.

As of June 30, 2010 and December 31, 2009, none of the
Companys investments were determined to be other than temporarily impaired.



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##### Table of Contents

Achillion Pharmaceuticals, Inc.

Notes to Financial Statements(Continued)

(in thousands, except per share amounts)

(Unaudited)



8. Accrued Expenses

Accrued expenses consist of the following:



|                                          |  |               |       |                   |   |      
|----------------------------------------- |  | ------------- | ----- | ----------------- | - | -----
|                                          |  | June 30, 2010 |       | December 31, 2009
|Accrued compensation                      |  | $             | 1,039 |                   | $ | 1,407
|Accrued research and development expenses |  |               | 744   |                   |   | 760  
|Accrued professional fees                 |  |               | 294   |                   |   | 296  
|Other accrued expenses                    |  |               | 108   |                   |   | 135  
|                                          |  |               |       |                   |   |      
|Total                                     |  | $             | 2,185 |                   | $ | 2,598
|                                          |  |               |       |                   |   |      

Accrued research and development expenses are
comprised of amounts owed to third-party contract research organizations or CROs, clinical investigators, laboratories and data managers for research and development work performed on behalf of the Company.

9. Debt

Debt consists
of the following:



|                                                                                                                                                                       |  |               |        |   |                   |   |        |  
|---------------------------------------------------------------------------------------------------------------------------------------------------------------------- |  | ------------- | ------ | - | ----------------- | - | ------ | -
|                                                                                                                                                                       |  | June 30, 2010 |        |   | December 31, 2009 |  
|Connecticut Innovations Term Loan, payable in monthly installments of $13 through September 2010 with a final balloon payment of
$686, with interest at 7.5% per annum |  | $             | 699    |   |                   | $ | 749    |  
|2003 Credit Facility, payable in monthly installments as the individual notes mature through December 2010, with interest ranging
from 7.75% to 9.06% per annum        |  |               | 76     |   |                   |   | 148    |  
|2008 Credit Facility, payable in monthly installments as notes mature through March 2011, with interest of 9.97% to
11.58% per annum                                   |  |               | 1,387  |   |                   |   | 2,387  |  
|                                                                                                                                                                       |  |               |        |   |                   |   |        |  
|Total debt                                                                                                                                                             |  |               | 2,162  |   |                   |   | 3,284  |  
|Less: current portion                                                                                                                                                  |  |               | (2,162 | ) |                   |   | (2,867 | )
|                                                                                                                                                                       |  |               |        |   |                   |   |        |  
|Total long-term debt, net of current portion                                                                                                                           |  | $             |       |   |                   | $ | 417    |  
|                                                                                                                                                                       |  |               |        |   |                   |   |        |  

The Company believes that the carrying value of our debt balances outstanding approximates fair value due to
the short term nature and fixed interest rates associated with each loan.

Each of the Companys debt agreements contains
certain subjective acceleration clauses, such that upon the occurrence of a material adverse change in the financial condition, business or operations of the Company in the view of the lenders, amounts outstanding under the agreement may become
immediately due and payable. At June 30, 2010, the Company believes the occurrence of a material adverse change is remote. The Company has no indication that it is in default of any such clauses, and none of the Companys lenders have
accelerated scheduled loan payments as a result of these provisions.

10. Stock-Based Compensation

The Companys 2006 Stock Incentive Plan, or the 2006 Plan, is administered by the Companys Board of Directors and provides for
the grant of incentive stock options, nonstatutory stock options, restricted stock, restricted stock units, stock appreciation rights and other stock-based awards. The Companys officers, employees, consultants, advisors and directors are
eligible to receive awards under the 2006 Plan; however, incentive stock options may only be granted to employees. Options granted are exercisable for a period determined by the Company, but in no event longer than ten years from the date of the
grant. Options generally vest ratably over four years. There were 3,725 shares available to be granted under the 2006 Plan as of June 30, 2010.



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##### Table of Contents

Achillion Pharmaceuticals, Inc.

Notes to Financial Statements(Continued)

(in thousands, except per share amounts)

(Unaudited)



A summary of the status of the Companys stock option activity for the six months
ended June 30, 2010 is presented in the table and narrative below:



|                                                                 |  |         |   |  |                              |     
|---------------------------------------------------------------- |  | ------- | - |  | ---------------------------- | ----
|                                                                 |  | Options |   |  | WeightedAverageExercisePrice
|Outstanding at January 1, 2010                                   |  | 3,320   |   |  | $                            | 4.10
|Granted                                                          |  | 25      |   |  |                              | 2.42
|Exercised                                                        |  |        |   |  |                              |    
|Cancelled/Forfeited                                              |  | (9      | ) |  |                              | 1.20
|                                                                 |  |         |   |  |                              |     
|Outstanding at June 30, 2010                                     |  | 3,336   |   |  | $                            | 4.09
|                                                                 |  |         |   |  |                              |     
|Options exercisable at June 30, 2010                             |  | 1,835   |   |  | $                            | 4.95
|                                                                 |  |         |   |  |                              |     
|Weighted-average fair value of options granted during the period |  |         |   |  | $                            | 1.78

The Company utilizes
the Black-Scholes option pricing model for determining the estimated fair value for stock-based awards. The Black-Scholes model requires the use of assumptions which determine the fair value of the stock-based awards. The assumptions used to value
options granted are as follows:



|                        |  |                          |   |  |               |  
|----------------------- |  | ------------------------ | - |  | ------------- | -
|                        |  | For the Six Months Ended |  
|                        |  | June 30, 2010            |   |  | June 30, 2009 |  
|Expected term of option |  | 6.1 years                |   |  | 6.1 years     |  
|Expected volatility     |  | 86                       | % |  | 79            | %
|Risk free interest rate |  | 2.92                     | % |  | 1.97          | %
|Expected dividend yield |  | 0                        | % |  | 0             | %

Total
compensation expense recorded in the accompanying statements of operations associated with option grants made to employees was $455 and $477 for the three months ended June 30, 2010 and 2009, respectively. Total compensation expense recorded in
the accompanying statements of operations associated with option grants made to employees was $913 and $950 for the six months ended June 30, 2010 and 2009, respectively. The Company recorded no tax benefit related to these options since the
Company currently maintains a full valuation allowance on its deferred tax assets.

As of June 30, 2010, the intrinsic
value of the options outstanding was $1,277, of which $655 related to vested options and $622 related to unvested options. The intrinsic value of stock options is calculated based on the difference between the exercise prices of the underlying
awards and the quoted stock price of the Companys common stock as of the reporting date.

As of June 30, 2010, the
total compensation cost related to unvested options not yet recognized in the financial statements is approximately $2,537, net of estimated forfeitures, and the weighted average period over which this amount is expected to be recognized is 1.4
years.

11. Comprehensive Loss

The Company reports and presents comprehensive loss in accordance with ASC 220, Comprehensive Income, which establishes standards
for reporting and display of comprehensive loss and its components in a full set of general purpose financial statements. The objective of the statement is to report a measure of all changes in equity of an enterprise that result from transactions
and other economic events of the period other than transactions with owners (comprehensive loss). The Companys other comprehensive loss arises from net unrealized gains (losses) on marketable securities.

Details relating to unrealized gains and losses and other comprehensive loss are as follows:



|                                                          |  |                                     |        |   |                                   |   |        |      |  |   |         |   |  |   |         |  
|--------------------------------------------------------- |  | ----------------------------------- | ------ | - | --------------------------------- | - | ------ | ---- |  | - | ------- | - |  | - | ------- | -
|                                                          |  | For the Three Months Ended June 30, |        |   | For the Six Months Ended June 30, |  
|                                                          |  | 2010                                |        |   | 2009                              |   |        | 2010 |  |   | 2009    |  
|Net loss                                                  |  | $                                   | (6,384 | ) |                                   | $ | (6,091 | )    |  | $ | (12,020 | ) |  | $ | (12,815 | )
|Change in unrealized gain (loss) on marketable securities |  |                                     | 1      |   |                                   |   | (36    | )    |  |   | (6      | ) |  |   | (103    | )
|                                                          |  |                                     |        |   |                                   |   |        |      |  |   |         |   |  |   |         |  
|Total comprehensive loss                                  |  | $                                   | (6,383 | ) |                                   | $ | (6,127 | )    |  | $ | (12,026 | ) |  | $ | (12,918 | )
|                                                          |  |                                     |        |   |                                   |   |        |      |  |   |         |   |  |   |         |  



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##### Table of Contents

Achillion Pharmaceuticals, Inc.

Notes to Financial Statements(Continued)

(in thousands, except per share amounts)

(Unaudited)



12. Stockholders Equity

Changes in stockholders equity for the six months ended June 30, 2010 and 2009 were as follows:



|                                                                |  |                                   |         |   |      |   |         |  
|--------------------------------------------------------------- |  | --------------------------------- | ------- | - | ---- | - | ------- | -
|                                                                |  | For the Six Months Ended June 30, |        
|                                                                |  | 2010                              |         |   | 2009 |  
|Balance at December 31, 2009 and 2008                           |  | $                                 | 1,022   |   |      | $ | 25,021  |  
|Net loss                                                        |  |                                   | (12,020 | ) |      |   | (12,815 | )
|Stock based compensation                                        |  |                                   | 938     |   |      |   | 976     |  
|Change in unrealized gain (loss) on marketable securities       |  |                                   | (6      | ) |      |   | (103    | )
|Issuance of common stock (see Note 4)                           |  |                                   | 22,628  |   |      |   |        |  
|Issuance of common stock under the Employee Stock Purchase Plan |  |                                   | 50      |   |      |   | 55      |  
|                                                                |  |                                   |         |   |      |   |         |  
|Balance at June 30, 2010 and 2009                               |  | $                                 | 12,612  |   |      | $ | 13,134  |  
|                                                                |  |                                   |         |   |      |   |         |  



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##### Table of Contents

|ITEM 2. | MANAGEMENTS DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS
|------- | -------------------------------------------------------------------------------------

This quarterly report on Form 10-Q contains forward-looking statements within the meaning of Section 21E of the Securities
Exchange Act of 1934, as amended, that involve risks and uncertainties. All statements other than statements relating to historical matters including statements to the effect that we believe, expect, anticipate,
plan, target, intend and similar expressions should be considered forward-looking statements. Our actual results could differ materially from those discussed in the forward-looking statements as a result of a
number of important factors, including factors discussed in this section and elsewhere in this quarterly report on Form 10-Q, including those discussed in Item 1A of this report under the heading Risk Factors, and the risks
discussed in our other filings with the Securities and Exchange Commission. Readers are cautioned not to place undue reliance on these forward-looking statements, which reflect managements analysis, judgment, belief or expectation only as the
date hereof. We assume no obligation to update these forward-looking statements to reflect events or circumstances that arise after the date hereof.

Overview

We are a biopharmaceutical company focused on the discovery, development and commercialization of innovative treatments for infectious
diseases. Within the anti-infective market, we are currently concentrating on the development of antivirals for the treatment of chronic hepatitis C and the development of antibacterials for the treatment of resistant bacterial infections. We are
currently focusing our efforts on developing four HCV drug candidates in three distinct classes: ACH-1625, a protease inhibitor for the treatment of chronic hepatitis C which recently completed phase Ib clinical testing, ACH-1095, a NS4A antagonist
also for the treatment of chronic hepatitis C, to which Gilead Sciences, Inc., or Gilead, retains certain future development rights, which is currently being prepared for IND filing, ACH-2684, a high-potency protease inhibitor which is currently in
preclinical testing, and ACH-2928, a NS5A inhibitor currently in preclinical testing. In addition, we have established a pipeline of certain other product candidates for which we are currently seeking additional appropriate collaborative partners,
but to which we are not devoting significant resources at this time. These product candidates include ACH-702 for the treatment of dermatologic and opthalmic infections and elvucitabine for the treatment of HIV infection.

We have devoted and are continuing to devote substantially all of our efforts toward product research and development. We have incurred
losses of $204 million from inception through June 30, 2010. Our net losses were $12.0 million and $12.8 million for the six months ended June 30, 2010 and 2009, respectively. We have funded our operations primarily through:



| |  |  | proceeds from the sale of equity securities, including our initial public offering in October 2006, a private placement of our common stock in August
2008 and a public offering of our common stock in January 2010;
| | - |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | borrowings from debt facilities; and
| | - |  | ------------------------------------



| |  |  | receipts from up-front and milestone payments, as well as cost-sharing receipts, from one of our collaboration partners, Gilead.
| | - |  | --------------------------------------------------------------------------------------------------------------------------------

In July 2009, we entered into a Standby Equity Distribution Agreement, or SEDA, with YA Global Master SPV
Ltd. pursuant to which we may, at our option, periodically sell YA Global shares of our common stock for a total purchase price of up to $15.0 million. For each share of common stock purchased under the SEDA, YA Global will pay us ninety-five
percent of the lowest volume-weighted average price of the common stock on the NASDAQ Global Market during the five consecutive trading days following our advance notice.

We expect to incur substantial and increasing losses for at least the next several years as we seek to:



| |  |  | continue clinical testing of ACH-1625;
| | - |  | --------------------------------------



| |  |  | finalize the clinical development plan for ACH-1095 and complete the necessary chemistry, manufacturing and control (CMC) activities in
order to file an investigational new drug (IND) application for this compound;
| | - |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | complete IND-enabling preclinical testing of ACH-2684 and ACH-2928; and
| | - |  | -----------------------------------------------------------------------



| |  |  | identify and progress additional drug candidates.
| | - |  | -------------------------------------------------

We will need substantial additional financing to obtain regulatory approvals, fund operating losses, and, if deemed appropriate,
establish manufacturing and sales and marketing capabilities, which we will seek to raise through public or private equity or debt financings, collaborative or other arrangements with third parties or through other sources of financing. There can be
no assurance that such funds will be available on terms favorable to us, if at all.



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##### Table of Contents

In addition to the normal risks associated with early-stage companies, there can be no
assurance that we will successfully complete our research and development, obtain adequate patent protection for our technology, obtain necessary government regulatory approval for drug candidates we develop, find and maintain appropriate
collaboration partners or that any approved drug candidates will be commercially viable. In addition, we may not be profitable even if we succeed in commercializing any of our drug candidates.

Financial Operations Overview

Revenue

To date, we have not generated revenue from the sale of any drugs. The majority of our revenue recognized to date has been derived from
our collaboration with Gilead to develop compounds for use in treating chronic hepatitis C. During the six months ended June 30, 2010 and 2009, we recognized $117,000 and $(300,000), respectively, under this collaboration agreement.

Upon initiating our collaboration with Gilead, we received a payment of $10.0 million, which included an equity investment by Gilead
determined to be worth approximately $2.0 million. The remaining $8.0 million is being accounted for as a nonrefundable up-front fee recognized under the proportionate performance model. Revenue under the proportionate performance model is
recognized as our effort under the collaboration is incurred. Payments made by us to Gilead in connection with this collaboration are being recognized as a reduction of revenue. When our performance obligation is complete, we will recognize
milestone payments, if any, when the corresponding milestone is achieved. We will recognize royalty payments, if any, upon product sales.

We did not recognize any amortization of deferred revenue during the six months ended June 30, 2010 and 2009, as we are currently
unable to accurately estimate our total performance obligations under the Gilead collaboration. We will determine if we are able to estimate our remaining total performance obligations when and if a new lead compound under the collaboration is
identified.

Effective April 1, 2007, each party provides for the costs of its own full-time equivalents. External
research costs continue to be shared equally by both parties. Through March 31, 2007, research and development expenses under our collaboration with Gilead, including internal full-time equivalent costs and external research costs, incurred by
both companies prior to proof-of-concept, were borne equally by both parties. As we were providing the majority of those services and were incurring the majority of those expenses, we were the net recipient of funds under this cost-sharing portion
of the arrangement and therefore recognized the reimbursed costs as revenue rather than research expense.

Through the
completion of our performance obligations under the collaboration with Gilead, we expect to recognize additional revenue of approximately $2.5 million, offset by any payments we are obligated to make to Gilead in satisfaction of external costs paid
by Gilead under our external cost-sharing arrangement. It is possible that we will recognize negative revenue in future quarters based upon the timing of our performance under the collaboration and on the timing and magnitude of external costs borne
by Gilead.

We have also recognized revenue under a Small Business Innovation Research, or SBIR, grant by the National
Institutes of Health, or NIH, for the further study of a back-up series of compounds related to ACH-702 for the treatment of tuberculosis infection. During the three and six months ended June 30, 2010 and June 30, 2009, we recognized
$144,000 and $0, respectively, of revenue under this grant.

Research and Development

Our research and development expenses reflect costs incurred for our proprietary research and development projects as well as costs for
research and development projects conducted as part of collaborative arrangements. These costs consist primarily of salaries and benefits for our research and development personnel, costs of services by clinical research organizations, other
outsourced research, materials used during research and development activities, facility-related costs such as rent and utilities associated with our laboratory and clinical development space and operating supplies.

We have established our current drug candidate pipeline primarily through our internal discovery capabilities except for elvucitabine,
which we in-license. Through both these efforts we have identified and are developing the following drug candidates and programs:



| |  |  | ACH-1625, a Protease Inhibitor for Chronic Hepatitis C Infection.We are evaluating ACH-1625, a protease inhibitor for the treatment of chronic
hepatitis C, in a phase Ib clinical trial to assess the compounds safety, tolerability, pharmacokinetic properties and efficacy in HCV-infected subjects. ACH-1625 has demonstrated strong potency, liver partitioning and a good safety profile in
preclinical studies. In both the phase Ia segments and the two phase Ib segments of a recent clinical trial, ACH-1625 was demonstrated to be safe and well-tolerated at total daily doses ranging from 50mg to 2000mg. Further, ACH-1625 was demonstrated
to significantly reduce viral load in HCV patients by 3.94 log10 and 4.25 log10 at doses of 600 mg twice daily and 500 mg twice daily, respectively. We anticipate that we will file an IND for ACH-1625 in the third quarter of 2010.
| | - |  | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



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##### Table of Contents

| |  |  | ACH-1095, a NS4A Antagonist for Chronic Hepatitis C Infection.We are evaluating ACH-1095 for the treatment of chronic hepatitis C. In
preclinical and clinical studies, NS4A antagonists demonstrate potent inhibition of the replication of HCV, by targeting a non-structural, or NS, viral protein called 4A. We believe these NS4A antagonists may offer several potential advantages
compared to currently available treatments, including greater potency, a novel mechanism of action, and lack of cross resistance. We believe these compounds could be used in combination with the current standard of care, or with other therapies in
development, to significantly improve treatment outcomes. Since November 2004, we have collaborated with Gilead under an exclusive license and collaboration agreement for the research, development and commercialization of compounds operating by this
mechanism of action. In May 2009, Gilead indicated that it did not intend to initiate clinical development of ACH-1095. We believe that the compound should be advanced. Therefore, in September 2009, we entered into an amendment to our license
and collaboration agreement with Gilead which allows us to continue to develop ACH-1095 independently and also provides that Gilead and Achillion will continue to advance additional compounds operating by the NS4A mechanism of action. We anticipate
that we will file an IND for ACH-1095 in the fourth quarter of 2010.
| | - |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | ACH-2684, a High-Potency Protease Inhibitor for Chronic Hepatitis C Infection.We are evaluating ACH-2684 for the treatment of chronic HCV
infection. In preclinical studies, ACH-2684 has demonstrated excellent potency in the low pico-molar range, as well as good pharmacokinetic and safety profiles. The potency and virology profiles of ACH-2684 demonstrate that it effectively suppresses
a broad range of natural variants of the hepatitis C virus, and may be effective in the prevention and treatment of emerging resistant variants. This compound also retains potent activity against all HCV genotypes. The very high potency of ACH-2684
was achieved by designing the compound to optimize the way in which it binds with NS3 protease. In vitro, ACH-2684 can be used in combination with other HCV inhibitors, and is synergistic with NS5B nucleoside polymerase inhibitors. ACH-2684 is
currently undergoing IND-enabling preclinical testing.
| | - |  | -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | ACH-2928, a NS5A Inhibitor for Chronic Hepatitis C Infection.We are advancing ACH-2928 in IND-enabling preclinical studies. In early
preclinical studies, ACH-2928 demonstrates excellent potency against HCV RNA replication, as well as good pharmacokinetic and safety profiles. The compound is highly active and retains potency against HCV genotypes 1a and 1b, as well as across other
genotypes. We believe its high potency, in the picomolar range, and its favorable pharmacokinetic properties, strongly suggest once-daily dosing. Importantly, ACH-2928 is highly effective in combination with NS3 protease inhibitors, NS5B polymerase
inhibitors, interferon and ribavirin.
| | - |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | ACH-702 for Drug Resistant Bacterial Infections. ACH-702 is a preclinical candidate with potency against a broad spectrum of bacterial pathogens
including methicillin-resistant staphylococcus aureus, or MRSA. In a pre-IND consultation with the FDA, we determined that the compound is most suited for dermatologic and ophthalmic use and use in medical biofilms. Due to resource constraints, at
this time, we do not anticipate moving into clinical development of ACH-702 for these indications and we do not expect to invest significantly in the future development of this compound without a collaboration partner or other external funding
source. We continue our research on compounds similar to ACH-702 for systemic use against MRSA and were recently awarded an SBIR grant for the further study of the compounds for the treatment of drug resistant tuberculosis.
| | - |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | Elvucitabine for HIV Infection. Elvucitabine is an antiviral being developed for the treatment of HIV infection. We have evaluated elvucitabine
in phase II clinical trials to further explore its safety and efficacy in HIV-infected patients up to 96-weeks of treatment and the open-label extension. We have licensed rights to develop and commercialize elvucitabine in China to GCA Therapeutics,
Ltd (GCAT) and we will be eligible to receive development milestones and royalties on net sales in those territories. We retain development and marketing rights to elvucitabine in other territories, and we are currently seeking other collaboration
arrangements for development and commercialization of elvucitabine in South Africa and South America. We do not plan to clinically advance elvucitabine independently.
| | - |  | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

All costs associated with internal research and development, and research and development services for which we have externally
contracted, are expensed as incurred. The costs of obtaining patents for our candidates are expensed as incurred as indirect costs.



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|                                          |  |                           |       |   |      |   |       |  
|----------------------------------------- |  | ------------------------- | ----- | - | ---- | - | ----- | -
|                                          |  | Six Months Ended June 30, |      
|                                          |  | 2010                      |       |   | 2009 |  
|                                          |  | (in thousands)            |      
|Clinical candidate direct external costs: |  |                           |       |   |      |   |       |  
|ACH-1625 (and related compounds)          |  | $                         | 2,667 |   |      | $ | 2,388 |  
|ACH-1095 (and related NS4A antagonists)   |  |                           | 244   |   |      |   | 162   |  
|ACH-2684                                  |  |                           | 471   |   |      |   |      |  
|ACH-702                                   |  |                           | 226   |   |      |   | 15    |  
|Elvucitabine                              |  |                           | 9     |   |      |   | 758   |  
|                                          |  |                           |       |   |      |   |       |  
|                                          |  |                           | 3,617 |   |      |   | 3,323 |  
|Direct internal personnel costs           |  |                           | 3,292 |   |      |   | 3,383 |  
|                                          |  |                           |       |   |      |   |       |  
|Sub-total direct costs                    |  |                           | 6,909 |   |      |   | 6,706 |  
|Indirect costs and overhead               |  |                           | 1,929 |   |      |   | 2,500 |  
|Research and development tax credit       |  |                           | (65   | ) |      |   | (70   | )
|                                          |  |                           |       |   |      |   |       |  
|Total research and development            |  | $                         | 8,773 |   |      | $ | 9,136 |  
|                                          |  |                           |       |   |      |   |       |  

We are currently initiating a phase IIa clinical trial of ACH-1625, completing IND-enabling studies of
ACH-2684 and continuing IND-enabling preclinical studies of ACH-2928.

The successful development of our drug candidates is
highly uncertain. At this time, we cannot reasonably estimate or know the nature, timing and estimated costs of the efforts that will be necessary to complete the remainder of the development of our drug candidates. We are also unable to predict
when, if ever, material net cash inflows will commence from any of our compounds.

We expect expenses associated with the
completion of these programs to be substantial and to increase. We do not believe, however, that it is possible at this stage of development to accurately project total program-specific expenses through commercialization. There are numerous factors
associated with the successful commercialization of any of our drug candidates, including future trial design and various regulatory requirements. Additionally, future commercial and regulatory factors beyond our control will evolve and therefore
impact our clinical development programs and plans over time.

General and Administrative

Our general and administrative expenses consist primarily of salaries and benefits for management and administrative personnel,
professional fees for legal, accounting and other services, travel costs and facility-related costs such as rent, utilities and other general office expenses.

Critical Accounting Standards and Estimates

The discussion and analysis of our financial condition and results of operations set forth below are based on our financial statements,
which have been prepared in accordance with accounting principles generally accepted in the United States, or U.S. GAAP. The preparation of these financial statements requires us to make estimates and assumptions that affect the reported amounts of
assets and liabilities and disclosure of contingent liabilities at the date of the financial statements and the reported amounts of revenues and expenses during the reporting period. On an ongoing basis, we evaluate our estimates and assumptions,
including those described below. We base our estimates on historical experience and on various other assumptions that we believe to be reasonable under the circumstances. These estimates and assumptions form the basis for making judgments about the
carrying values of assets and liabilities that are not readily apparent from other sources. Management makes estimates and exercises judgment in revenue recognition, research and development costs, stock-based compensation, accrued expenses and
income taxes. Actual results may differ from these estimates under different assumptions or conditions.



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We believe the following critical accounting policies affect managements more
significant judgments and estimates used in the preparation of our financial statements:

Revenue Recognition

We recognize revenue from contract research and development and research progress payments in accordance with ASC 605,
Revenue Recognition. Revenue-generating research and development collaborations are often multiple element arrangements, providing for a license as well as research and development services. Such arrangements are analyzed to determine whether
the deliverables, including research and development services, can be separated or whether they must be accounted for as a single unit of accounting. We recognize upfront license payments as revenue upon delivery of the license only if the license
has standalone value and the fair value of the undelivered performance obligations can be determined. If the fair value of the undelivered performance obligations can be determined, such obligations would then be accounted for separately as
performed. If the license is considered to either (i) not have standalone value or (ii) have standalone value but the fair value of any of the undelivered performance obligations cannot be determined, the arrangement would then be
accounted for as a single unit of accounting and the upfront license payments are recognized as revenue over the estimated period of when our performance obligations are performed.

When we determine that an arrangement should be accounted for as a single unit of accounting, we must determine the period over which the
performance obligations will be performed and revenue related to upfront license payments will be recognized. Revenue will be recognized using either a proportionate performance or straight-line method. We recognize revenue using the proportionate
performance method provided that we can reasonably estimate the level of effort required to complete our performance obligations under an arrangement and such performance obligations are provided on a best-efforts basis. Under the proportionate
performance method, periodic revenue related to up-front license payments is recognized as the percentage of actual effort expended in that period to total effort expected for all of our performance obligations under the arrangement. Actual effort
is generally determined based upon actual direct labor hours or full-time equivalents (FTE) incurred and include research and development activities performed by internal scientists. Total expected effort is generally based upon the
total direct labor hours of FTEs incorporated into the detailed budget and project plan that is agreed to by both parties to the collaboration. Significant management judgment is required in determining the level of effort required under an
arrangement and the period over which we expect to complete the related performance obligations. In the event that a change in estimate occurs, the change will be accounted for using the cumulative catch-up method which provides for an adjustment to
revenue in the current period. Estimates of our level of effort may change in the future, resulting in a material change in the amount of revenue recognized in future periods, including negative revenue in some periods. If Gilead elects not to
participate in further development of ACH-1095 and elects not to pursue additional back-up compounds, we will then recognize the remaining balance of deferred revenue relating to upfront, milestone and FTE payments received under the collaboration.

Generally under collaboration arrangements, payments received during the period of performance may include up-front payments,
time-or performance-based milestones and reimbursement of internal and external costs. The proportion of actual performance to total expected performance is applied to these payments in determining periodic revenue, but will be limited by the
aggregate cash received or receivable to date.

Substantive milestone payments are considered to be performance bonuses that
are recognized upon achievement of the milestone only if all of the following conditions are met: (1) the milestone payments are non-refundable, (2) achievement of the milestone involves a degree of risk and was not reasonably assured at
the inception of the arrangement, (3) substantive effort is involved in achieving the milestone, (4) the amount of the milestone payment is reasonable in relation to the effort expended or the risk associated with achievement of the
milestone and (5) a reasonable amount of time passes between the upfront license payment and the first milestone payment as well as between each subsequent milestone payment.

Reimbursement of costs is recognized as revenue provided the amounts are determinable and collection of the related receivable is
reasonably assured. Amounts owed to Gilead for external costs are treated as contra revenue.

We revised our joint research
program with Gilead in the first quarter of 2009 at which time we extended the period over which our remaining obligations under the arrangement would be completed, thereby increasing our total estimated efforts under the collaboration. At the
current time, we cannot accurately estimate our future obligations under the collaboration as we have not identified a new lead compound that will be developed jointly. Therefore, during the six months ended June 30, 2010 and 2009, we did not
recognize any revenue from upfront, milestone and FTE fees previously received under the collaboration. We will determine if we are able to estimate our remaining total performance obligations when and if a new lead compound under the collaboration
is identified.



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In September 2009, we and Gilead amended our collaboration arrangement so that we may
continue to develop ACH-1095 independently during an Interim Period, while Gilead may join us in developing ACH-1095 at clinical proof-of-concept, as defined. We will bear all costs associated with ACH-1095 development during the Interim
Period. If Gilead elects to regain rights to ACH-1095, Gilead will reimburse us for all ACH-1095 development costs incurred during the Interim Period, and all original milestone and royalty payments described in the License Agreement will again
apply to ACH-1095. Gilead is under no obligation to exercise its right with respect to ACH-1095. If Gilead elects not to exercise its right to ACH-1095 within forty-five (45) days after proof-of-concept, we shall gain all rights to ACH-1095 and
Gilead will then have the right to designate a new lead compound. We continue to be responsible for back-up activities, which included preclinical assessment of a limited number of other NS4A antagonists. Gilead will otherwise be responsible for all
manufacturing, formulation and commercialization activities associated with such compounds, if nominated, including all regulatory filings and clinical trials after proof-of-concept.

Stock-Based Compensation  Employee Stock-Based Awards

We apply ASC 718, Stock Compensation,which requires measurement and recognition of compensation expense for all stock-based awards
made to employees and directors, including employee stock options and employee stock purchases under our 2006 ESPP Plan based on estimated fair values. Due to our limited exercise history and the period of time that our shares have been publicly
traded, we utilize the simplified method in developing an estimate of the expected term of plain vanilla share options.

We primarily grant qualified stock options for a fixed number of shares to employees with an exercise price equal to the market value of
the shares at the date of grant. To the extent that the amount of the aggregate fair market value of qualified stock options that become exercisable for an individual exceeds $100,000 during any tax year, those stock options are treated as non
qualified stock options. Under the fair value recognition provisions, stock-based compensation cost is based on the value of the portion of stock-based awards that is ultimately expected to vest. Stock-based compensation expense recognized during
the six months ended June 30, 2009 includes compensation expense for stock-based awards granted prior to, but not yet vested as of December 31, 2005, as well as amounts related to the stock-based awards granted subsequent to
December 31, 2005, based on the fair value on the grant date.

We utilize the Black-Scholes option pricing model for
determining the estimated fair value for stock-based awards. The Black-Scholes model requires the use of assumptions which determine the fair value of the stock-based awards. Determining the fair value of stock-based awards at the grant date
requires judgment, including estimating the expected term of stock options, the expected volatility of our stock and expected dividends. In addition, we are required to estimate forfeitures at the grant date and recognize compensation costs for only
those awards that are expected to vest. Judgment is required in estimating the amount of stock-based awards that are expected to be forfeited.

If factors change and we employ different assumptions in future periods, the compensation expense that we record may differ significantly
from what we have recorded in the current period. Therefore, we believe it is important for investors to be aware of the degree of subjectivity involved when using option pricing models to estimate share-based compensation. There is risk that our
estimates of the fair values of our share-based compensation awards on the grant dates may differ from the actual values realized upon the exercise, expiration, early termination or forfeiture of those share-based payments in the future. Certain
share-based payments, such as employee stock options, may expire worthless or otherwise result in zero intrinsic value as compared to the fair values originally estimated on the grant date and reported in our financial statements. Alternatively,
value may be realized from these instruments that is significantly in excess of the fair values originally estimated on the grant date and reported in our financial statements. Although the fair value of employee share-based awards is determined
using an option pricing model, that value may not be indicative of the fair value observed in a willing buyer/willing seller market transaction.

Accrued Expenses

As part of the process of preparing financial statements, we are required to estimate accrued expenses. This process involves identifying
services which have been performed on our behalf and estimating the level of service performed and the associated cost incurred for such service as of each balance sheet date in our financial statements.

In accruing service fees, we estimate the time period over which services will be provided and the level of effort in each period. If the
actual timing of the provision of services or the level of effort varies from the estimate, we will adjust the accrual accordingly. The majority of our service providers invoice us monthly in arrears for services performed. Some of our service
providers require upfront or milestone payments. If our estimate of services performed is less than the upfront or milestone payments, the difference is accounted for as a prepaid expense. In the event that we do not identify costs that have been
incurred or we underestimate or overestimate the level of services performed or the costs of such services, our actual expenses could differ



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from such estimates. The date on which some services commence, the level of services performed on or before a given date and the cost of such services are often subjective determinations. We make
judgments based upon facts and circumstances known to us in accordance with U.S. GAAP.

Income Taxes

We use an asset and liability approach for financial accounting and reporting of income taxes. Deferred tax assets and liabilities are
determined based on temporary differences between financial reporting and tax basis assets and liabilities and are measured by applying enacted rates and laws to taxable years in which differences are expected to be recovered or settled. Further,
the effect on deferred tax assets and liabilities of a change in tax rates is recognized in income in the period that the rate changes. A valuation allowance is required when it is more likely than not that all or a portion of deferred
tax assets will not be realized.

We apply the provisions of ASC 740, Income Taxes,which prescribes a comprehensive
model for how a company should recognize, measure, present and disclose in its financial statements uncertain tax positions that the company has taken or expects to take on a tax return, including a decision whether to file or not file a return in a
particular jurisdiction. Our financial statements reflect expected future tax consequences of such positions presuming the taxing authorities full knowledge of the position and all relevant facts.

We do not have any unrecognized tax benefits as of June 30, 2010. We review all tax positions to ensure the tax treatment selected
is sustainable based on its technical merits and that the position would be sustained if challenged.

Results of
Operations

Results of operations may vary from period to period depending on numerous factors, including the timing of
payments received under existing or future strategic alliances, joint ventures or financings, if any, the progress of our research and development projects, technological advances and determinations as to the commercial potential of proposed
products.

Comparison of Three and Six Months Ended June 30, 2010 and 2009

Revenue. Revenue was $187,000 and $(7,000) for the three months ended June 30, 2010 and 2009, respectively, and $261,000 and
$(300,000) for the six months ended June 30, 2010 and 2009, respectively. The increase in revenue in 2010 is due to lower external costs incurred by Gilead, under our collaboration, which are shared by us and recorded as a reduction in revenue,
combined with the recognition of revenue related to our SBIR grant for the further study and characterization of our series of compounds related to ACH-702. During the three and six months ended June 30, 2009, external costs incurred by Gilead
exceeded external costs incurred by us, resulting in a net payable from us to Gilead and negative revenue for the period.

Because we are currently unable to estimate our future performance obligations under our collaboration with Gilead, we have ceased
recognizing revenue related to upfront, milestone and FTE payments previously received until we can reasonably estimate our total future performance obligations under the collaboration. We will determine if we are able to estimate our remaining
future performance obligations when and if a new lead candidate under the collaboration is identified. Under the proportionate performance method, periodic revenue related to upfront license and milestone payments is recognized as the percentage of
actual effort expended in that period to total effort expected for all of our performance obligations under the arrangement. Additionally, under the collaboration arrangement, external costs are shared equally by both parties and payments we make to
Gilead are recognized as a reduction of revenue. Revenue for the three and six months ended June 30, 2010 and 2009 is comprised as follows:



|                             |  |                             |     |                           |   |    |        |  |      |  |      |     |  |        |      |   |  |   |    
|---------------------------- |  | --------------------------- | --- | ------------------------- | - | -- | ------ |  | ---- |  | ---- | --- |  | ------ | ---- | - |  | - | ---
|                             |  | Three Months Ended June 30, |     | Six Months Ended June 30,
|                             |  | 2010                        |     | 2009                      |   |    | Change |  | 2010 |  | 2009 |     |  | Change
|                             |  | (in thousands)              |     | (in thousands)           
|Gilead collaboration revenue |  | $                           | 43  |                           | $ | (7 | )      |  | 50   |  | $    | 117 |  | $      | (300 | ) |  | $ | 417
|Grant revenue                |  |                             | 144 |                           |   |   |        |  | 144  |  |      | 144 |  |        |     |   |  |   | 144
|                             |  |                             |     |                           |   |    |        |  |      |  |      |     |  |        |      |   |  |   |    
|Total revenue                |  | $                           | 187 |                           | $ | (7 | )      |  | 194  |  | $    | 261 |  | $      | (300 | ) |  | $ | 561
|                             |  |                             |     |                           |   |    |        |  |      |  |      |     |  |        |      |   |  |   |    



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Through the completion of our performance obligations under the collaboration with Gilead,
we expect to recognize additional revenue of approximately $2.5 million. It is possible that we will recognize negative revenue in future quarters based upon the timing of our performance under the collaboration and on the timing and magnitude of
external costs borne by Gilead.

Research and Development Expenses. Research and development expenses were $4.8 million
and $4.4 million for the three months ended June 30, 2010 and 2009, respectively, and $8.8 million and $9.1 million for the six months ended June 30, 2010 and 2009, respectively. The increase for the three months ended June 30, 2010
was primarily due to increased expenses related to clinical testing of ACH-1625 and ACH-2684 preclinical studies, offset by decreased clinical trial costs related to elvucitabine. The decrease for the six months ended June 30, 2010 was
primarily due to decreased facilities costs related to our reduction of leased laboratory and office space combined with lower intellectual property costs and lower costs resulting from our July 2009 reduction in workforce. We expect research and
development expenses to increase during the remainder of the year as we continue clinical testing of ACH-1625, complete the necessary CMC activities for ACH-1095, complete IND-enabling preclinical testing for ACH-2684 and continue IND-enabling
preclinical testing for ACH-2928. Research and development expenses for the three and six months ended June 30, 2010 and 2009 are comprised as follows:



|                                    |  |                             |       |   |                           |   |       |        |  |   |      |   |  |      |       |   |        |   |       |   |  |   |      |  
|----------------------------------- |  | --------------------------- | ----- | - | ------------------------- | - | ----- | ------ |  | - | ---- | - |  | ---- | ----- | - | ------ | - | ----- | - |  | - | ---- | -
|                                    |  | Three Months Ended June 30, |       |   | Six Months Ended June 30, |  
|                                    |  | 2010                        |       |   | 2009                      |   |       | Change |  |   | 2010 |   |  | 2009 |       |   | Change |  
|Personnel costs                     |  | $                           | 1,410 |   |                           | $ | 1,440 |        |  | $ | (30  | ) |  | $    | 2,912 |   |        | $ | 3,005 |   |  | $ | (93  | )
|Stock based compensation            |  |                             | 188   |   |                           |   | 190   |        |  |   | (2   | ) |  |      | 378   |   |        |   | 378   |   |  |   |     |  
|Outsourced research and supplies    |  |                             | 2,320 |   |                           |   | 1,764 |        |  |   | 556  |   |  |      | 3,615 |   |        |   | 3,577 |   |  |   | 38   |  
|Professional and consulting fees    |  |                             | 339   |   |                           |   | 327   |        |  |   | 12   |   |  |      | 709   |   |        |   | 801   |   |  |   | (92  | )
|Facilities costs                    |  |                             | 517   |   |                           |   | 663   |        |  |   | (146 | ) |  |      | 1,117 |   |        |   | 1,361 |   |  |   | (244 | )
|Travel and other costs              |  |                             | 75    |   |                           |   | 45    |        |  |   | 30   |   |  |      | 107   |   |        |   | 84    |   |  |   | 23   |  
|Research and development tax credit |  |                             | (35   | ) |                           |   | (30   | )      |  |   | (5   | ) |  |      | (65   | ) |        |   | (70   | ) |  |   | 5    |  
|                                    |  |                             |       |   |                           |   |       |        |  |   |      |   |  |      |       |   |        |   |       |   |  |   |      |  
|Total                               |  | $                           | 4,814 |   |                           | $ | 4,399 |        |  | $ | 415  |   |  | $    | 8,773 |   |        | $ | 9,136 |   |  | $ | (363 | )
|                                    |  |                             |       |   |                           |   |       |        |  |   |      |   |  |      |       |   |        |   |       |   |  |   |      |  

We reclassified certain prior period amounts to conform to the current years presentation. State
research and development credit carryforwards that were exchanged for cash of $30,000 and $70,000 were reclassified from income tax benefit to a reduction of research and development expenditures for the three months and six months ended
June 30, 2009, respectively.

General and Administrative Expenses. General and administrative expenses were $1.7
million and $1.6 million for the three months ended March 31, 2010 and 2009, respectively, and $3.4 million and $3.2 million for the six months ended June 30, 2010 and 2009, respectively. The increase for the three months ended was
primarily due to increased personnel and travel costs related to the addition of business development personnel. The increase for the six months ended June 30, 2010 was primarily due to increased personnel and travel costs related to the
addition of business development personnel combined with increased corporate fees, offset primarily by decreased facilities costs related to our reduction of leased laboratory and office space and professional fees. We expect that general and
administrative expenses will be consistent for the remainder of the year. General and administrative expenses for the three and six months ended June 30, 2010 and 2009 are comprised as follows:



|                                 |  |                             |       |      |                           |        |  |   |      |   |      |   |        |  |   |       |  |   |     |  
|-------------------------------- |  | --------------------------- | ----- | ---- | ------------------------- | ------ |  | - | ---- | - | ---- | - | ------ |  | - | ----- |  | - | --- | -
|                                 |  | Three Months Ended June 30, |       |      | Six Months Ended June 30, |       
|                                 |  | 2010                        |       | 2009 |                           | Change |  |   | 2010 |   | 2009 |   | Change | 
|Personnel costs                  |  | $                           | 596   |      | $                         | 538    |  | $ | 58   |   |      | $ | 1,240  |  | $ | 1,090 |  | $ | 150 |  
|Stock based compensation         |  |                             | 279   |      |                           | 300    |  |   | (21  | ) |      |   | 560    |  |   | 598   |  |   | (38 | )
|Professional and consulting fees |  |                             | 356   |      |                           | 359    |  |   | (3   | ) |      |   | 654    |  |   | 693   |  |   | (39 | )
|Facilities costs                 |  |                             | 282   |      |                           | 295    |  |   | (13  | ) |      |   | 519    |  |   | 573   |  |   | (54 | )
|Travel and other costs           |  |                             | 177   |      |                           | 106    |  |   | 71   |   |      |   | 384    |  |   | 247   |  |   | 137 |  
|                                 |  |                             |       |      |                           |        |  |   |      |   |      |   |        |  |   |       |  |   |     |  
|Total                            |  | $                           | 1,690 |      | $                         | 1,598  |  | $ | 92   |   |      | $ | 3,357  |  | $ | 3,201 |  | $ | 156 |  
|                                 |  |                             |       |      |                           |        |  |   |      |   |      |   |        |  |   |       |  |   |     |  

Other Income (Expense). Interest income was $15,000 and $57,000 for the three months ended
June 30, 2010 and 2009, respectively. The decrease was primarily due to decreased average cash balances. Interest expense was $82,000 and $144,000 for the three months ended June 30, 2010 and 2009, respectively. The decrease was primarily
due to lower average debt facility balances outstanding in 2010.



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Interest income was $25,000 and $149,000 for the six months ended June 30, 2010 and
2009, respectively. The decrease was primarily due to decreased average cash balances. Interest expense was $176,000 and $327,000 for the six months ended June 30, 2010 and 2009, respectively. The decrease was primarily due to lower average
debt facility balances outstanding in 2010.

Liquidity and Capital Resources

Since our inception in August 1998, we have financed our operations primarily through the issuance of stock and borrowings under debt
facilities, as well as through receipts from our collaboration with Gilead. Through June 30, 2010, we have received approximately $214.9 million in aggregate net proceeds from stock issuances, including convertible preferred stock, our initial
public offering, our 2008 private placement and our 2010 public offering, $19.2 million from Gilead under our collaboration agreement and approximately $22.1 million under debt facilities. As of June 30, 2010, amounts remain outstanding under
the following debt facilities:



|                                     |  |               |  |                          |   |  |                 |           |               |                   
|------------------------------------ |  | ------------- |  | ------------------------ | - |  | --------------- | --------- | ------------- | ------------------
|Lender                               |  | Date          |  | Interest Rate(per annum) |   |  | PrincipalAmount |           | Maturity Date
|Connecticut Innovations, Inc.        |  | November 2000 |  | 7.50                     | % |  | $               | 1,400,000 |               | September 2010    
|Webster Bank                         |  | May 2003      |  | 6.72 - 9.27              | % |  |                 | 1,386,883 |               | June 2006-Dec 2010
|Oxford Finance Corporation           |  | June 2007     |  | 11.58                    | % |  |                 | 400,000   |               | July 2010         
|General Electric Capital Corporation |  | June 2007     |  | 11.58                    | % |  |                 | 400,000   |               | July 2010         
|Oxford Finance Corporation           |  | February 2008 |  | 9.97                     | % |  |                 | 2,500,000 |               | March 2011        
|General Electric Capital Corporation |  | February 2008 |  | 9.97                     | % |  |                 | 2,500,000 |               | March 2011        

The amounts
reflected above represent original maturities under our debt agreements. As of June 30, 2010, our debt balance was $2.2 million with a weighted average interest rate of 9.26%.

We had $19.5 million and $9.7 million in cash, cash equivalents and marketable securities as of June 30, 2010 and December 31,
2009, respectively. We regularly review our investments and monitor the financial markets. The recent distress in the financial markets has not had a significant impact on our financial position. As of June 30, 2010, our cash, cash equivalents
and marketable securities included high-quality financial instruments, primarily money market funds, government sponsored bond obligations and government-backed and certain other corporate debt securities which we believe are subject to limited
credit risk.

Cash used in operating activities was $11.5 million for the six months ended June 30, 2010 and was
primarily attributable to our $12.0 million net loss combined with an increase in prepaid expense and a decrease in accrued expenses, offset primarily by non-cash charges related to depreciation, amortization and non-cash stock-based compensation.
Cash used in operating activities was $12.7 million for the six months ended June 30, 2009 and was primarily attributable to our $12.8 million net loss and a decrease in accounts payable and accrued expenses, offset primarily by non-cash
charges related to depreciation, amortization and non-cash stock based compensation.

Cash used in investing activities was
$5.5 million for the six months ended June 30, 2010 and was primarily attributable to the purchase of marketable securities. Cash provided by investing activities was $12.9 million for the six months ended June 30, 2009 and was primarily
attributable to the maturities of marketable securities partially offset by purchases of marketable securities.

Cash provided
by financing activities was $21.5 million for the six months ended June 30, 2010 and was primarily attributable to $22.6 million in net proceeds from the sale of 11,816,250 shares of common stock in January and February 2010, offset by
repayments of debt. Cash used in financing activities was $1.9 million for the six months ended June 30, 2009 and was primarily attributable to repayments of debt.

We expect to incur continuing and increasing losses from operations for at least the next several years as we seek to:



| |  |  | continue clinical testing of ACH-1625;
| | - |  | --------------------------------------



| |  |  | finalize the clinical development plan for ACH-1095 and complete the necessary chemistry, manufacturing and control (CMC) activities in
order to file an investigational new drug (IND) application for this compound;
| | - |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | complete IND-enabling preclinical testing of ACH-2684 and ACH-2928; and
| | - |  | -----------------------------------------------------------------------



22



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##### Table of Contents

| |  |  | identify and progress additional drug candidates.
| | - |  | -------------------------------------------------

We do not expect our existing capital resources, together with the milestone payments and research and development funding we expect to
receive, to be sufficient to fund the completion of the development of any of our drug candidates. As a result, we will need to raise additional funds prior to among other things, being able to market any drug candidates, to obtain regulatory
approvals, fund operating losses, and, if deemed appropriate, establish manufacturing and sales and marketing capabilities. We will seek to raise such additional financing through (i) public or private equity or debt financings,
(ii) collaborative or other arrangements with third parties or (iii) other sources of financing.

We believe that
our existing cash and cash equivalents, as potentially augmented by the SEDA or additional financing activities, will be sufficient to meet our projected operating requirements through at least June 30, 2011. However, our funding resources and
requirements may change and will depend upon numerous factors, including but not limited to:



| |  |  | the costs involved in the clinical development, manufacturing and formulation of ACH-1625;
| | - |  | ------------------------------------------------------------------------------------------



| |  |  | the costs associated with IND preparation, including the required CMC work, related to ACH-1095;
| | - |  | ------------------------------------------------------------------------------------------------



| |  |  | the costs associated with the preclinical development and manufacturing of ACH-2684 and ACH-2928;
| | - |  | -------------------------------------------------------------------------------------------------



| |  |  | the partnership opportunities for ACH-702 that we may pursue;
| | - |  | -------------------------------------------------------------



| |  |  | our ability to enter into corporate collaborations and the terms and success of these collaborations;
| | - |  | -----------------------------------------------------------------------------------------------------



| |  |  | the costs involved in obtaining regulatory approvals for our drug candidates;
| | - |  | -----------------------------------------------------------------------------



| |  |  | the scope, prioritization and number of programs we pursue;
| | - |  | -----------------------------------------------------------



| |  |  | the costs involved in preparing, filing, prosecuting, maintaining, enforcing and defending patent and other intellectual property claims;
| | - |  | -----------------------------------------------------------------------------------------------------------------------------------------



| |  |  | our ability to raise incremental debt or equity capital, including any changes in the credit market that may impact our ability to obtain capital in
the future;
| | - |  | ----------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | our acquisition and development of new technologies and drug candidates; and
| | - |  | ----------------------------------------------------------------------------



| |  |  | competing technological and market developments currently unknown to us.
| | - |  | ------------------------------------------------------------------------

In January 2010, we issued 10,275,000 shares of our common stock in an underwritten public offering. In February 2010, we issued an
additional 1,541,250 shares of common stock in connection with the underwriters exercise of an over-allotment option. We received net proceeds of $22.6 million from these share issuances.

We intend to augment our cash balance through financing transactions, including the issuance of debt or equity securities, and/or further
corporate alliances. There can be no assurance that we will be able to obtain adequate levels of additional funding or favorable terms, if at all. If adequate funds are not available, we will be required to:



| |  |  | delay, reduce the scope of or eliminate additional research and development programs;
| | - |  | -------------------------------------------------------------------------------------



| |  |  | obtain funds through arrangements with collaborators or others on terms unfavorable to us or that may require us to relinquish rights to certain drug
candidates that we might otherwise seek to develop or commercialize independently; and/or
| | - |  | -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | pursue merger or acquisition strategies.
| | - |  | ----------------------------------------

Any future equity funding may dilute the ownership of our equity investors.

Additionally, each of our debt agreements contains certain subjective acceleration clauses, such that upon the occurrence of a material
adverse change in our financial condition, business or operations in the view of the lenders, amounts outstanding under the agreement may become immediately due and payable. We believe that the occurrence of a material change is remote and we have
no indication that it we are in default of any such clauses. Additionally, none of our lenders have accelerated scheduled loan payments as a result of these provisions.

Off-Balance Sheet Arrangements

We do not have any off-balance sheet arrangements or relationships with unconsolidated entities or financial partnerships, such as
entities often referred to as structured finance or special purpose entities.



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Recently Issued Accounting Standards

In October 2009, an update was made to ASC 605,Revenue Recognition,which provides accounting principles and application guidance
on how revenue arrangements with multiple deliverables should be separated and the consideration allocated. This guidance eliminates the requirement to establish the fair value of undelivered products and services for separate revenue recognition.
Allocation of consideration is now based on managements estimate of the selling price for an undelivered item where there is no other means to determine the fair value of that undelivered item. This update is effective prospectively for
revenue arrangements entered into or materially modified in fiscal years beginning on or after June 15, 2010. Early adoption of this update is permitted; however, we will be required to apply the provisions of the amendment retrospectively to
the beginning of our fiscal year. We are currently evaluating the potential impact of this standard on our financial position and results of operations.

In January 2010, the Financial Accounting Standards Board (FASB) issued Accounting Standards Update (ASU) 2010-06
which amended guidance on fair value measurement and disclosures. The new guidance requires additional disclosures regarding fair value measurements and provides clarification regarding the level of disaggregation of fair value disclosures by
investment class. This guidance is effective for reporting periods beginning after December 15, 2009 except for the additional level 3 requirements which is effective for reporting periods beginning after December 15, 2010. There was no
impact to our financial statements upon adoption.

In April 2010, the FASB issued Accounting Standard Update
No. 2010-17,Milestone Method of Revenue Recognition, which provides guidance on applying the milestone method to milestone payments for achieving specified performance measures when those payments are related to uncertain future events.
However, the FASB clarified that, even if the requirements in this ASU are met, entities would not be precluded from making an accounting policy election to apply another appropriate accounting policy that results in the deferral of some portion of
the arrangement consideration. The ASU is effective for periods beginning on or after June 15, 2010. Early application was permitted. Entities can apply this guidance retrospectively as well as prospectively to milestones achieved after
adoption. There was no impact to our financial statements upon adoption.



|ITEM 3. | QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK
|------- | ----------------------------------------------------------

Interest Rate Risk. Our exposure to market risk is confined to our cash, cash equivalents and marketable securities. We regularly
review our investments and monitor the financial markets. We do not believe the recent distress in the financial markets has had a significant impact on our financial position. We invest in high-quality financial instruments, primarily money market
funds, government sponsored bond obligations and government backed corporate debt securities, with the effective duration of the portfolio less than six months and no security with an effective duration in excess of twelve months, which we believe
are subject to limited credit risk. We currently do not hedge interest rate exposure. Due to the short-term nature of our investments, we do not believe that we have any material exposure to interest rate risk or changes in credit ratings arising
from our investments.

Capital Market Risk. We currently have no product revenues and depend on funds raised through
other sources. One source of funding is through future equity offerings. Our ability to raise funds in this manner depends upon capital market forces affecting our stock price.



|ITEM 4. | CONTROLS AND PROCEDURES
|------- | -----------------------

Our management, with the participation of our chief executive officer and chief financial officer, evaluated the effectiveness of our
disclosure controls and procedures as of June 30, 2010. The term disclosure controls and procedures, as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, or the Exchange Act, means controls and
other procedures of a company that are designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is recorded, processed, summarized and reported within the time periods
specified in the SECs rules and forms. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by a company in the reports that it files or submits
under the Exchange Act is accumulated and communicated to the companys management, including its principal executive and principal financial officers, as appropriate to allow timely decisions regarding required disclosure. Management
recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives and management necessarily applies its judgment in evaluating the cost-benefit relationship of
possible controls and procedures. Based on the evaluation of our disclosure controls and procedures as of June 30, 2010, our chief executive officer and chief financial officer concluded that, as of such date, our disclosure controls and
procedures were effective at the reasonable assurance level.



24



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##### Table of Contents

No change in our internal control over financial reporting (as defined in
Rules 13a15(d) and 15d15(d) under the Exchange Act) occurred during the fiscal quarter ended June 30, 2010 that has materially affected, or is reasonably likely to materially affect, our internal control over financial
reporting.

PART II. OTHER INFORMATION



|ITEM 1A. | RISK FACTORS
|-------- | ------------

You
should carefully consider the risks described below in addition to the other information contained in this report, before making an investment decision. Our business, financial condition or results of operations could be harmed by any of these
risks. The risks and uncertainties described below are not the only ones we face. Additional risks not currently known to us or other factors not perceived by us to present significant risks to our business at this time also may impair our business
operations.

Risks Related to Our Business

We depend on the success of our HCV drug candidates, which are still under development.

We have invested a significant portion of our efforts and financial resources in the development of our HCV candidates, ACH-1625,
ACH-1095, ACH-2684 and ACH-2928, for the treatment of chronic hepatitis C infection. Our ability to generate revenues will depend heavily on the successful development and commercialization of these drug candidates. The development and commercial
success of these drug candidates will depend on several factors, including the following:



| |  |  | our ability to provide acceptable evidence of the safety and efficacy of these drug candidates in current and future clinical trials;
| | - |  | -------------------------------------------------------------------------------------------------------------------------------------



| |  |  | our ability to develop drug formulations that will deliver the appropriate drug exposures in longer term clinical trials;
| | - |  | -------------------------------------------------------------------------------------------------------------------------



| |  |  | receipt of marketing approvals from the FDA and similar foreign regulatory authorities;
| | - |  | ---------------------------------------------------------------------------------------



| |  |  | establishing commercial manufacturing arrangements with third-party manufacturers;
| | - |  | ----------------------------------------------------------------------------------



| |  |  | launching commercial sales of the drugs, whether alone or in collaboration with others;
| | - |  | ---------------------------------------------------------------------------------------



| |  |  | acceptance of the drug in the medical community and with third-party payors; and
| | - |  | --------------------------------------------------------------------------------



| |  |  | our ability to identify, enter into and maintain collaboration agreements with appropriate strategic partners for our compounds.
| | - |  | --------------------------------------------------------------------------------------------------------------------------------

We are initiating a phase IIa clinical trial for ACH-1625, are completing preclinical studies of ACH-2684
and are continuing preclinical studies of ACH-2928. Positive results from clinical trials or in preclinical studies of a drug candidate may not be predictive of similar results in human clinical trials, and promising results from early clinical
trials of a drug candidate may not be replicated in later clinical trials. Our most advanced HCV compound, ACH-1625, has been tested in human clinical trials for periods no longer than five days. A number of companies in the pharmaceutical and
biotechnology industries have suffered significant setbacks in late-stage clinical trials even after achieving promising results in early-stage development. Accordingly, the results from the preclinical studies of ACH-1625, ACH-2684 or ACH-2928 or
the completed clinical trials for ACH-1625 may not be predictive of the results we may obtain in later stage trials.

We
anticipate that we will file an IND for ACH-1625 in the third quarter of 2010 and for ACH-1095 in the fourth quarter of 2010. To date, clinical trials of ACH-1625 have been conducted in Europe under a clinical trial application, or CTA, approved by
the health authorities of Belgium and Muldova. There can be no assurance that we will gain FDA approval of the IND applications for these compounds, and if we are not able to advance these compounds, our business may be significantly harmed. Even if
we obtain FDA approval of the IND applications, the clinical development timelines and costs may be greater than anticipated. Further, there can be no assurance that planned long term toxicology studies in animals will indicate a safety and
tolerability profile appropriate for continued dosing in human subjects.

We do not expect any of our drug candidates to be
commercially available for at least several years, if at all.

We have a limited operating history and have incurred a
cumulative loss since inception. If we do not generate significant revenues, we will not be profitable.

We have incurred
significant losses since our inception in August 1998. As of June 30, 2010, our accumulated deficit was approximately $218 million. We have not generated any revenue from the sale of drug candidates to date. We expect that our annual operating
losses will increase over the next several years as we expand our research, development and commercialization efforts.



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##### Table of Contents

To become profitable, we must successfully develop and obtain regulatory approval for our
drug candidates and effectively manufacture, market and sell any drug candidates we develop. Accordingly, we may never generate significant revenues and, even if we do generate significant revenues, we may never achieve profitability.

We will need substantial additional capital to fund our operations, including drug candidate development, manufacturing and
commercialization. If we do not have or cannot raise additional capital when needed, we will be unable to develop and commercialize our drug candidates successfully, and our ability to operate as a going concern may be adversely affected.

We believe that our existing cash and cash equivalents, as potentially augmented by the SEDA or other financing
activities, will be sufficient to support our current operating plan through at least June 30, 2011. Our operating plan may change as a result of many factors, including:



| |  |  | the costs involved in the clinical development, manufacturing and formulation of ACH-1625;
| | - |  | ------------------------------------------------------------------------------------------



| |  |  | the costs associated with IND preparation, including the required CMC work, related to ACH-1095;
| | - |  | ------------------------------------------------------------------------------------------------



| |  |  | the costs associated with the preclinical development and manufacturing of ACH-2684 and ACH-2928;
| | - |  | -------------------------------------------------------------------------------------------------



| |  |  | the partnership opportunities we may pursue for ACH-702;
| | - |  | --------------------------------------------------------



| |  |  | our ability to enter into corporate collaborations and the terms and success of these collaborations;
| | - |  | -----------------------------------------------------------------------------------------------------



| |  |  | the costs involved in obtaining regulatory approvals for our drug candidates;
| | - |  | -----------------------------------------------------------------------------



| |  |  | the scope, prioritization and number of programs we pursue;
| | - |  | -----------------------------------------------------------



| |  |  | the costs involved in preparing, filing, prosecuting, maintaining, enforcing and defending patent and other intellectual property claims;
| | - |  | -----------------------------------------------------------------------------------------------------------------------------------------



| |  |  | our ability to raise incremental debt or equity capital, including any changes in the credit market that may impact our ability to obtain capital in
the future;
| | - |  | ----------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | our acquisition and development of new technologies and drug candidates; and
| | - |  | ----------------------------------------------------------------------------



| |  |  | competing technological and market developments currently unknown to us.
| | - |  | ------------------------------------------------------------------------

If our operating plan changes, we may need additional funds sooner than planned. Such additional financing may not be available when we
need it or may not be available on terms that are favorable to us. In addition, we may seek additional capital due to favorable market conditions or strategic considerations, even if we believe we have sufficient funds for our current or future
operating plans. If adequate funds are not available to us on a timely basis, or at all, we may be required to:



| |  |  | terminate or delay preclinical studies, clinical trials or other development activities for one or more of our drug candidates; or
| | - |  | ----------------------------------------------------------------------------------------------------------------------------------



| |  |  | delay our establishment of sales and marketing capabilities or other activities that may be necessary to commercialize our drug candidates, if approved
for sale.
| | - |  | -----------------------------------------------------------------------------------------------------------------------------------------------------------------

We may seek additional financing through a combination of private and public equity offerings,
debt financings and collaboration, strategic alliance and licensing arrangements. To the extent that we raise additional capital through the sale of equity or convertible debt securities or through SEDA advances, your ownership interest will be
diluted, and the terms may include adverse liquidation or other preferences that adversely affect your rights as a stockholder. For example, in January 2010 and February 2010, we issued an aggregate of 11,816,250 shares of our common stock resulting
in gross proceeds to us of $24.6 million. Additionally, in August 2008, we issued in a private placement 10,714,655 shares of our common stock, plus common stock warrants to purchase a total of 2,678,644 additional shares of stock, resulting in
gross proceeds to us of $31.1 million. These offerings substantially diluted our existing stockholders. Stockholders will be further diluted if, and to the extent, any investors from the August 2008 private placement exercise their warrants. Debt
financing, if available, may involve covenants that limit or restrict our ability to take specific actions such as incurring additional debt, making capital expenditures or declaring dividends, or may involve immediate repayment of the debt under
certain circumstances. For example, each of our debt agreements contains certain subjective acceleration clauses, such that upon the occurrence of a material adverse change in our financial condition, business or operations in the view of the
lenders, amounts outstanding under the agreement may become immediately due and payable. If we raise additional funds through collaborations, strategic alliances and licensing arrangements with third parties, we may have to relinquish valuable
rights to our technologies or drug candidates, or grant licenses on terms that are not favorable to us.



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Our market is subject to intense competition. If we are unable to compete effectively,
our drug candidates may be rendered noncompetitive or obsolete.

We are engaged in segments of the pharmaceutical industry
that are highly competitive and rapidly changing. Many large pharmaceutical and biotechnology companies, academic institutions, governmental agencies and other public and private research organizations are pursuing the development of novel drugs
that target infectious diseases. We face, and expect to continue to face, intense and increasing competition as new products enter the market and advanced technologies become available. In addition to currently approved drugs, there are a
significant number of drugs that are currently under development and may become available in the future for the treatment of chronic hepatitis C, serious hospital-based bacterial infections and HIV infection. We would expect ACH-1625, ACH-1095,
ACH-2684, ACH-2928, ACH-702 and elvucitabine to compete with the following approved drugs and drug candidates currently under development:



| |  |  | If approved, our protease inhibitors, ACH-1625 and ACH-2684, our NS4A antagonist, ACH-1095, and our NS5A inhibitor, ACH-2928, would compete with drugs
currently approved for the treatment of hepatitis C, the interferon-alpha-based products from Roche (Pegasys and Roferon-A) or Schering- Plough (Intron-A or Peg-Intron) and the ribavirin based products from Schering-Plough (Rebetrol), Roche
(Copegus) or generic versions sold by various companies. In addition, our HCV compounds may compete with the interferon and ribavirin-based drugs currently in development such as Valeants ribavirin analog (Viramidine) and Human Genome
Sciences Albuferon. Other products in multiple classes including protease inhibitors, polymerase inhibitors (nucleoside and non-nucleoside), NS5A inhibitors, toll-like receptors and cyclophilin inhibitors are also under development for the
treatment of hepatitis C by companies such as Abbott, Anadys, Astra-Zeneca, Avila Therapeutics, Boehringer Ingelheim, Bristol-Myers Squibb, Enanta, Gilead, GlaxoSmithKline, Human Genome Sciences, Idenix, Intermune, Johnson & Johnson,
Presidio, Medivir, Merck, Novartis, Pfizer, Pharmasset, Roche, Valeant and Vertex.
| | - |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | ACH-702, if developed and approved, would compete with drugs currently marketed for the treatment of tuberculosis infections including first-line
drugs: Nydrazid (isoniazid) by Sandoz Pharmaceuticals, Rifadin (rifampin) by Sanofi-Aventis, Myambutol (ethambutol) by X-Gen Pharmaceuticals and Pyrazinamide (pyrazinamide) by Effcon Laboratories or second-line drugs: Avelox (moxifloxacin) by Bayer,
Amikacin (amikacin) by Teva Pharmaceuticals, Kantrex (kanamycin) by Bristol-Myers Squibb, Capastat (capreomycin) by Eli Lilly, Cipro (ciprofloxacin) by Bayer, Trecator (ethionamide) by Wyeth, Seromycin (cycloserine) by Eli Lilly, and PASER
(p-aminosalicylic acid) by Jacobus Pharmaceuticals. In addition, ACH-702 may compete with other drugs currently under development for the treatment of tuberculosis infections including: PA-824 by Chiron/Novartis and TMC207 by Tibotec
Pharmaceuticals. In addition, ACH-702 may compete with other drugs currently marketed or under development for the treatment of topical skin infections including Altabax by GlaxoSmithKline and XOMA-629 by Xoma Therapeutics Ltd. and may compete with
drugs for serious ophthalmic infections including: Besivance by Bausch and Lomb, Vigamox by Alcon Pharmaceuticals and Zymar by Allergan. We may also compete with the following companies that have a strategic interest in the discovery, development
and marketing of drugs for the treatment of bacterial infections: Abbott, Astra-Zeneca, Aventis, Bristol-Myers Squibb, Cubist, Eli Lilly, GlaxoSmithKline, Merck, Novartis, Pfizer, Roche and Wyeth.
| | - |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | Elvucitabine, if developed and approved, elvucitabine would compete with the NRTIs currently marketed for treatment of HIV infection, including: Epivir
(lamivudine), Retrovir (AZT), Ziagen (abacavir), Combivir (lamivudine + AZT), Trizivir (lamivudine + AZT + abacavir) and Epzicom (lamivudine + abacavir) from GlaxoSmithKline, Hivid (ddC) from Hoffman-La Roche, Emtriva (FTC), Viread (tenofovir) and
Truvada (FTC + tenofovir) from Gilead and Videx EC, Videx (ddI) and Zerit (d4T) from Bristol-Myers Squibb. In addition, elvucitabine may compete with other NRTIs currently under development for HIV by companies such as Avexa, Medivir, and Koronis.
Other drugs in other classes recently approved for treatment of HIV infection include Selzentry (miraviroc, an entry inhibitor) from Pfizer and Isentress (raltegravir, an integrase inhibitor) from Merck. In addition, there are other classes of drugs
under development for the treatment of HIV infection by companies such as Abbott, Boehringer Ingelheim, GlaxoSmithKline, Johnson & Johnson, Myriad, Roche and Schering-Plough.
| | - |  | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Many of our competitors have:



| |  |  | significantly greater financial, technical and human resources than we have and may be better equipped to discover, develop, manufacture and
commercialize drug candidates;
| | - |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | more extensive experience in preclinical testing and clinical trials, obtaining regulatory approvals and manufacturing and marketing pharmaceutical
products;
| | - |  | -------------------------------------------------------------------------------------------------------------------------------------------------------------



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| |  |  | drug candidates that have been approved or are in late-stage clinical development; and/or
| | - |  | -----------------------------------------------------------------------------------------



| |  |  | collaborative arrangements in our target markets with leading companies and research institutions.
| | - |  | --------------------------------------------------------------------------------------------------

Competitive products may render our products obsolete or noncompetitive before we can recover the expenses of developing and
commercializing our drug candidates. Furthermore, the development of new treatment methods and/or the widespread adoption or increased utilization of any vaccine for the diseases we are targeting could render our drug candidates noncompetitive,
obsolete or uneconomical. If we successfully develop and obtain approval for our drug candidates, we will face competition based on the safety and effectiveness of our drug candidates, the timing of their entry into the market in relation to
competitive products in development, the availability and cost of supply, marketing and sales capabilities, reimbursement coverage, price, patent position and other factors. If we successfully develop drug candidates but those drug candidates do not
achieve and maintain market acceptance, our business will not be successful.

If we are not able to attract and retain key
management, scientific personnel and advisors, we may not successfully develop our drug candidates or achieve our other business objectives.

We depend upon our senior management and scientific staff for our business success. Key members of our senior team include Michael
Kishbauch, our president and chief executive officer, and Dr. Milind Deshpande, our executive vice president and chief scientific officer. All of our employment agreements with our senior management employees are terminable without notice by
the employee. The loss of the service of any of the key members of our senior management may significantly delay or prevent the achievement of drug development and other business objectives. Our ability to attract and retain qualified personnel,
consultants and advisors is critical to our success. We face intense competition for qualified individuals from numerous pharmaceutical and biotechnology companies, universities, governmental entities and other research institutions. We may be
unable to attract and retain these individuals, and our failure to do so would adversely affect our business.

Our business
has a substantial risk of product liability claims. If we are unable to obtain appropriate levels of insurance, a product liability claim could adversely affect our business.

Our business exposes us to significant potential product liability risks that are inherent in the development, manufacturing and sales
and marketing of human therapeutic products. Although we do not currently commercialize any products, claims could be made against us based on the use of our drug candidates in clinical trials. Product liability claims could delay or prevent
completion of our clinical development programs. We currently have clinical trial insurance in an amount equal to up to $10.0 million in the aggregate and will seek to obtain product liability insurance prior to the sales and marketing of any of our
drug candidates. However, our insurance may not provide adequate coverage against potential liabilities. Furthermore, clinical trial and product liability insurance is becoming increasingly expensive. As a result, we may be unable to maintain
current amounts of insurance coverage or obtain additional or sufficient insurance at a reasonable cost to protect against losses that could have a material adverse effect on us. If a claim is brought against us, we might be required to pay legal
and other expenses to defend the claim, as well as uncovered damages awards resulting from a successful claim. Furthermore, whether or not we are ultimately successful in defending any such claims, we might be required to direct significant
financial and managerial resources to such defense, and adverse publicity is likely to result.

Risks Related to the
Development of Our Drug Candidates

All of our drug candidates are still in the early stages of development and
remain subject to clinical testing and regulatory approval. If we are unable to successfully develop, test and commercialize our drug candidates, we will not be successful.

To date, we have not commercially marketed, distributed or sold any drug candidates. The success of our business depends primarily upon
our ability to develop and commercialize our drug candidates successfully. Our drug candidates must satisfy rigorous standards of safety and efficacy before they can be approved for sale. To satisfy these standards, we must engage in expensive and
lengthy testing and obtain regulatory approval of our drug candidates. Despite our efforts, our drug candidates may not:



| |  |  | offer therapeutic or other improvement over existing, comparable drugs;
| | - |  | -----------------------------------------------------------------------



| |  |  | be proven safe and effective in clinical trials;
| | - |  | ------------------------------------------------



| |  |  | have the desired effects, or may include undesirable effects or may have other unexpected characteristics;
| | - |  | ----------------------------------------------------------------------------------------------------------



| |  |  | meet applicable regulatory standards;
| | - |  | -------------------------------------



| |  |  | be capable of being produced in commercial quantities at acceptable costs; or
| | - |  | -----------------------------------------------------------------------------



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| |  |  | be successfully commercialized.
| | - |  | -------------------------------

In addition, we may experience numerous unforeseen events during, or as a result of, preclinical testing and the clinical trial process
that could delay or prevent our ability to receive regulatory approval or commercialize our drug candidates, including:



| |  |  | regulators or Institutional Review Boards, or IRBs, may not authorize us to commence a clinical trial or conduct a clinical trial at a prospective
trial site;
| | - |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | our preclinical tests or clinical trials for our drug candidates may produce negative or inconclusive results, and we may decide, or regulators may
require us, to conduct additional preclinical testing or clinical trials, or we may abandon projects that we expect to be promising;
| | - |  | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | enrollment in our clinical trials may be slower than we currently anticipate or participants may drop out of our clinical trials at a higher rate than
we currently anticipate, resulting in significant delays;
| | - |  | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | our third-party contractors may fail to comply with regulatory requirements or meet their contractual obligations to us in a timely manner;
| | - |  | -------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | we might have to suspend or terminate our clinical trials if the participants are exposed to unacceptable health risks;
| | - |  | -----------------------------------------------------------------------------------------------------------------------



| |  |  | IRBs or regulators, including the FDA, may require that we hold, suspend or terminate clinical research for various reasons, including noncompliance
with regulatory requirements; and
| | - |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | the supply or quality of our drug candidates or other materials necessary to conduct our clinical trials may be insufficient or inadequate.
| | - |  | -------------------------------------------------------------------------------------------------------------------------------------------

We, and a number of other companies in the pharmaceutical and biotechnology industries, have suffered
significant setbacks in later stage clinical trials even after achieving promising results in early-stage development. For example, in February 2007, we announced that we discontinued further clinical development of ACH-806, our first NS4A
antagonist candidate, which was determined to have positive antiviral effect in a proof-of-concept clinical trial in HCV infected patients, but also to elevate serum creatinine levels, a marker of kidney function. There can be no assurance that we
have identified the source of the serum creatinine elevation and that we will not see a similar outcome in human clinical trials with that programs successor compound, ACH-1095 or that observations in preclinical studies of ACH-1095 in one
species may not limit or even preclude its clinical use. Accordingly, there can be no assurance that this, or another type of toxicity, will not arise in future clinical trials.

In December 2009, we requested a consultation with the FDA to discuss the most appropriate clinical development path for ACH-1095. In
February 2010, we received a response from the FDA. On the basis of that response, we will respond to the FDAs comments, incorporate FDA guidance into the clinical protocol, and address certain manufacturing and formulation issues that need to
be completed in the final IND. We anticipate that we will file an IND for ACH-1095 in the fourth quarter of 2010. There can be no assurance that we will gain the agencys approval of the IND application for ACH-1095, and if we are not able to
advance ACH-1095, our business may be significantly harmed. Even if we are successful in gaining FDA approval of our IND application for ACH-1095 and advance to human clinical trials, the clinical development timelines and costs may be greater than
anticipated. Further, there can be no assurance that planned long term toxicology studies in animals will indicate a safety and tolerability profile appropriate for continued dosing in human subjects. We do not expect any of our drug candidates to
be commercially available for several years.

If clinical trials for our drug candidates are prolonged or delayed, we may
be unable to commercialize our drug candidates on a timely basis, which would require us to incur additional costs and delay our receipt of any product revenue.

We cannot predict whether we will encounter problems with any of our completed, ongoing or planned clinical trials that will cause us or
regulatory authorities to delay, suspend or terminate clinical trials, or delay the analysis of data from our completed or ongoing clinical trials. Any of the following could delay the clinical development of our drug candidates:



| |  |  | ongoing discussions with the FDA or comparable foreign authorities regarding the scope or design of our clinical trials;
| | - |  | ------------------------------------------------------------------------------------------------------------------------



| |  |  | delays in receiving, or the inability to obtain, required approvals from institutional review boards or other reviewing entities at clinical sites
selected for participation in our clinical trials;
| | - |  | -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | delays in enrolling volunteers and patients into clinical trials;
| | - |  | -----------------------------------------------------------------



| |  |  | a lower than anticipated retention rate of volunteers and patients in clinical trials;
| | - |  | --------------------------------------------------------------------------------------



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| |  |  | the need to repeat clinical trials as a result of inconclusive or negative results or unforeseen complications in testing;
| | - |  | --------------------------------------------------------------------------------------------------------------------------



| |  |  | inadequate supply or deficient quality of drug candidate materials or other materials necessary to conduct our clinical trials;
| | - |  | -------------------------------------------------------------------------------------------------------------------------------



| |  |  | unfavorable FDA inspection and review of a clinical trial site or records of any clinical or preclinical investigation;
| | - |  | -----------------------------------------------------------------------------------------------------------------------



| |  |  | serious and unexpected drug-related side effects experienced by participants in our clinical trials; or
| | - |  | -------------------------------------------------------------------------------------------------------



| |  |  | the placement by the FDA of a clinical hold on a trial.
| | - |  | -------------------------------------------------------

Our ability to enroll patients in our clinical trials in sufficient numbers and on a timely basis will be subject to a number of factors,
including the size of the patient population, the nature of the protocol, the proximity of patients to clinical sites, the availability of effective treatments for the relevant disease and the eligibility criteria for the clinical trial. Delays in
patient enrollment may result in increased costs and longer development times. For example, in 2007 we experienced delays in patient enrollment in connection with our phase II trial of elvucitabine in HIV infected patients who have failed a HAART
regimen which included Epivir (lamivudine) due to the strict entry criteria for this trial. As a result, we expanded the number of sites at which the trial was conducted and changed the protocol of the trial to include additional treatment with
elvucitabine after the initial 14 days of treatment. We may also face competition for subjects to enroll in our ACH-1625 clinical trials and may have to expand the number of sites at which the trials are conducted. As a result, we may incur
increased costs and longer development times for these trials. In addition, subjects may drop out of our clinical trials, and thereby impair the validity or statistical significance of the trials.

We, the FDA or other applicable regulatory authorities may suspend clinical trials of a drug candidate at any time if we or they believe
the subjects or patients participating in such clinical trials are being exposed to unacceptable health risks or for other reasons.

We cannot predict whether any of our drug candidates will encounter problems during clinical trials which will cause us or regulatory
authorities to delay or suspend these trials, or which will delay the analysis of data from these trials. In addition, it is impossible to predict whether legislative changes will be enacted, or whether FDA regulations, guidance or interpretations
will be changed, or what the impact of such changes, if any, may be. If we experience any such problems, we may not have the financial resources to continue development of the drug candidate that is affected or the development of any of our other
drug candidates.

In addition, we, along with our collaborators or subcontractors, may not employ, in any capacity, persons
who have been debarred under the FDAs Application Integrity Policy. Employment of such a debarred person (even if inadvertently) may result in delays in the FDAs review or approval of our products, or the rejection of data developed with
the involvement of such persons.

Even if we obtain regulatory approvals, our drug candidates will be subject to ongoing
regulatory review. If we fail to comply with continuing U.S. and applicable foreign regulations, we could lose those approvals, and our business would be seriously harmed.

Even if we receive regulatory approval of any drugs we are developing or may develop, we will be subject to continuing regulatory review,
including the review of clinical results which are reported after our drug candidates become commercially available approved drugs. As greater numbers of patients use a drug following its approval, side effects and other problems may be observed
after approval that were not seen or anticipated during pre-approval clinical trials. In addition, the manufacturer, and the manufacturing facilities we use to make any approved drugs, will also be subject to periodic review and inspection by the
FDA. The subsequent discovery of previously unknown problems with the drug, manufacturer or facility may result in restrictions on the drug, manufacturer or facility, including withdrawal of the drug from the market. If we fail to comply with
applicable continuing regulatory requirements, we may be subject to fines, suspension or withdrawal of regulatory approval, product recalls and seizures, operating restrictions and criminal prosecutions.

Our product promotion and advertising is also subject to regulatory requirements and continuing regulatory review. In particular, the
marketing claims we will be permitted to make in labeling or advertising regarding our marketed products will be limited by the terms and conditions of the FDA-approved labeling. We must submit copies of our advertisements and promotional labeling
to the FDA at the time of initial publication or dissemination. If the FDA believes these materials or statements promote our products for unapproved indications, or with unsubstantiated claims, or if we fail to provide appropriate safety-related
information, the FDA could allege that our promotional activities misbrand our products. Specifically, the FDA could issue an untitled letter or warning letter, which may demand, among other things, that we cease such promotional activities and
issue corrective advertisements and labeling. The FDA also could take enforcement action including seizure of allegedly misbranded product, injunction or criminal prosecution against us and our officers or employees. If we repeatedly or deliberately
fail to submit



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such advertisements and labeling to the agency, the FDA could withdraw our approvals. Moreover, the Department of Justice can bring civil or criminal actions against companies that promote drugs
or biologics for unapproved uses, based on the False Claims Act and other federal laws governing reimbursement for such products under the Medicare, Medicaid and other federally supported healthcare programs. Monetary penalties in such cases have
often been substantial, and civil penalties can include costly mandatory compliance programs and exclusion from federal healthcare programs.

If we do not comply with laws regulating the protection of the environment and health and human safety, our business could be
adversely affected.

Our research and development efforts involve the controlled use of hazardous materials, chemicals and
various radioactive compounds. Although we believe that our safety procedures for the use, manufacture, storage, handling and disposing of these materials comply with the standards prescribed by federal, state and local laws and regulations, the
risk of accidental contamination or injury from these materials cannot be eliminated. If an accident occurs, we could be held liable for resulting damages, which could be substantial. We are also subject to numerous environmental, health and
workplace safety laws and regulations, including those governing laboratory procedures, exposure to blood-borne pathogens and the handling of biohazardous materials.

Additional federal, state and local laws and regulations affecting our operations may be adopted in the future. Although we maintain
workers compensation insurance to cover us for costs we may incur due to injuries to our employees resulting from the use of these materials, this insurance may not provide adequate coverage against potential liabilities. In addition, though
we have environmental liability insurance, such coverage may not provide for all related losses. We may incur substantial costs to comply with, and substantial fines or penalties if we violate any of these laws or regulations.

Risks Relating to Our Securities

We may be required to dilute our existing stockholders further in connection with capital raising activities. Additionally, the market
price of our common stock may fall due to the increased number of shares available in the public market.

In connection
with capital raising activities, we may be required to dilute our existing stockholders substantially. For example, in January and February 2010, we issued an aggregate of 11,816,250 shares of our common stock in an underwritten offering.
Additionally, in August 2008, we issued 10,714,655 shares of our common stock, plus common stock warrants to purchase a total of 2,678,644 additional shares of stock in a private placement. Stockholders will be further diluted if, and to the extent,
any investors exercise their warrants. The issuance of these shares and warrants resulted in substantial dilution to stockholders who held our common stock prior to the issuance. All of the shares of common stock we issued, as well as those shares
issuable upon exercise of the warrants, are freely tradable pursuant to registration statements filed with the SEC that were declared effective by the SEC on October 30, 2008 and October 16, 2009, making such shares available for immediate
resale in the public market.

We also entered into a Standby Equity Distribution Agreement with YA Global Master SPV Ltd. on
July 1, 2009 whereby we have the option, at our sole discretion, to sell up to $15.0 million of common stock to YA Global. The sale of shares of our common stock pursuant to the SEDA will have a dilutive impact on our stockholders and may cause
the market price of our common stock to decline.

In addition, amounts remain available for the future issuance of common
stock, preferred stock and/or warrants that we may issue from time to time under the shelf registration statement on Form S-3 that we filed in October 2009. If we issue additional securities pursuant to this shelf registration statement, these
securities would be available for immediate resale in the public market.

The market price of our common stock could fall due
to an increase in the number of shares available for sale in the public market.

Our executive officers, directors and
principal stockholders own a large percentage of our voting common stock and could limit our stockholders influence on corporate decisions or could delay or prevent a change in corporate control.

As of August 1, 2010, our directors, executive officers and current holders of more than 5% of our outstanding common stock,
together with their affiliates and related persons, beneficially own, in the aggregate, approximately 73% of our outstanding common stock. As a result, these stockholders, if acting together, have the ability to determine the outcome of all matters
submitted to our stockholders for approval, including the election and removal of directors and any merger, consolidation or sale of all or substantially all of our assets and other extraordinary transactions. The interests of this group of
stockholders may not



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always coincide with our corporate interests or the interest of other stockholders, and they may act in a manner with which you may not agree or that may not be in the best interests of other
stockholders. This concentration of ownership may have the effect of:



| |  |  | delaying, deferring or preventing a change in control of our company;
| | - |  | ---------------------------------------------------------------------



| |  |  | entrenching our management and/or board;
| | - |  | ----------------------------------------



| |  |  | impeding a merger, consolidation, takeover or other business combination involving our company; or
| | - |  | --------------------------------------------------------------------------------------------------



| |  |  | discouraging a potential acquirer from making a tender offer or otherwise attempting to obtain control of our company.
| | - |  | ----------------------------------------------------------------------------------------------------------------------

Our stock price is likely to be volatile, and the market price of our common stock may decline in value in the future.

The market price of our common stock has fluctuated in the past and is likely to fluctuate in the future. During the period from
January 1, 2007 to June 30, 2010 our closing stock price has ranged from a low of $0.68 to a high of $19.61. Market prices for securities of early stage pharmaceutical, biotechnology and other life sciences companies have historically been
particularly volatile. Some of the factors that may cause the market price of our common stock to fluctuate include:



| |  |  | the results of our planned clinical trials of ACH-1625;
| | - |  | -------------------------------------------------------



| |  |  | the timing of our IND preparation, including the required CMC work, related to ACH-1095;
| | - |  | ----------------------------------------------------------------------------------------



| |  |  | the results of our preclinical development and manufacturing of ACH-2684 and ACH-2928;
| | - |  | --------------------------------------------------------------------------------------



| |  |  | the entry into, modification of, or termination of key agreements, or any new collaboration agreement we may enter;
| | - |  | -------------------------------------------------------------------------------------------------------------------



| |  |  | the results of regulatory reviews relating to the approval of our drug candidates;
| | - |  | ----------------------------------------------------------------------------------



| |  |  | the initiation of, material developments in, or conclusion of litigation to enforce or defend any of our intellectual property rights;
| | - |  | --------------------------------------------------------------------------------------------------------------------------------------



| |  |  | failure of any of our drug candidates, if approved, to achieve commercial success;
| | - |  | ----------------------------------------------------------------------------------



| |  |  | general and industry-specific economic conditions that may affect our research and development expenditures;
| | - |  | ------------------------------------------------------------------------------------------------------------



| |  |  | the results of clinical trials conducted by others on drugs that would compete with our drug candidates;
| | - |  | --------------------------------------------------------------------------------------------------------



| |  |  | the failure or discontinuation of any of our research programs;
| | - |  | ---------------------------------------------------------------



| |  |  | issues in manufacturing our drug candidates or any approved products;
| | - |  | ---------------------------------------------------------------------



| |  |  | the introduction of technological innovations or new commercial products by us or our competitors;
| | - |  | --------------------------------------------------------------------------------------------------



| |  |  | changes in estimates or recommendations by securities analysts who cover our common stock;
| | - |  | ------------------------------------------------------------------------------------------



| |  |  | future sales of our common stock;
| | - |  | ---------------------------------



| |  |  | changes in the structure of health care payment systems;
| | - |  | --------------------------------------------------------



| |  |  | period-to-period fluctuations in our financial results; and
| | - |  | -----------------------------------------------------------



| |  |  | low trading volume of our common stock.
| | - |  | ---------------------------------------

In addition, if we fail to reach an important research, development or commercialization milestone or result by a publicly expected
deadline, even if by only a small margin, there could be significant impact on the market price of our common stock. Additionally, as we approach the announcement of important clinical data or other significant information and as we announce such
results and information, we expect the price of our common stock to be particularly volatile, and negative results would have a substantial negative impact on the price of our common stock.

The stock markets in general have experienced substantial volatility that has often been unrelated to the operating performance of
individual companies. These broad market fluctuations may adversely affect the trading price of our common stock.

In the
past, following periods of volatility in the market price of a companys securities, stockholders have often instituted class action securities litigation against those companies. Such litigation, if instituted, could result in substantial
costs and diversion of management attention and resources, which could significantly harm our business operations and reputation.



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If we do not comply with Nasdaqs listing requirements, our common stock could be
delisted from the Nasdaq Global Market, which would negatively impact our liquidity, our stockholders ability to sell shares and our ability to raise capital.

Our listing on the Nasdaq Global Market is conditioned upon our compliance with the Nasdaq Marketplace Rules. On November 13, 2009,
we received notification from the NASDAQ Listings Qualification Department that our stockholders equity of $7,214,000, as reported on our Quarterly Report on Form 10-Q for the quarter ended September 30, 2009 did not comply with the
minimum stockholders equity requirement of $10,000,000 for continued listing on The NASDAQ Global Market. On December 14, 2009, we received notification from the NASDAQ Listings Qualification Department that we had regained compliance for
continued listing on The NASDAQ Global Market based on compliance with the market value standard. If the price of our common stock declines and we are unable to raise additional equity, we may once again receive a notification from the NASDAQ
Listings Qualification Department that our stockholders equity does not comply with the minimum stockholders equity requirement for continued listing on The NASDAQ Global Market. The delisting of our common stock would significantly
affect the ability of investors to trade our securities and would significantly and negatively affect the value and liquidity of our common stock. In addition, the delisting of our common stock could materially and adversely affect our ability to
raise capital on terms acceptable to us or at all. Delisting from the NASDAQ Global Market could also have other negative results, including the potential loss of confidence by suppliers and employees, the loss of institutional investor interest and
fewer business development opportunities.

Unstable market and economic conditions may have serious adverse consequences on
our business.

Our general business strategy may be adversely affected by the recent economic downturn and volatile
business environment and continued unpredictable and unstable market conditions. If the current equity and credit markets deteriorate further, or do not improve, it may make any necessary debt or equity financing more difficult, more costly, and
more dilutive. Failure to secure any necessary financing in a timely manner and on favorable terms could have a material adverse effect on our growth strategy, financial performance and stock price and could require us to delay or abandon clinical
development plans. In addition, there is a risk that one or more of our current service providers, manufacturers and other partners may not survive these difficult economic times, which would directly affect our ability to attain our operating goals
on schedule and on budget.

Our management is required to devote substantial time and incur additional expense to comply
with public company regulations. Our failure to comply with such regulations could subject us to public investigations, fines, enforcement actions and other sanctions by regulatory agencies and authorities and, as a result, our stock price could
decline in value.

Prior to our initial public offering in 2006, as a private company with limited resources, we
maintained a small finance and accounting staff. As a public company, the Sarbanes-Oxley Act of 2002 and the related rules and regulations of the SEC, as well as the rules of the Nasdaq Global Market, have required us to implement additional
corporate governance practices and adhere to a variety of reporting requirements and complex accounting rules. Compliance with these public company obligations places significant additional demands on our limited number of finance and accounting
staff and on our financial, accounting and information systems.

In particular, as a public company, our management is
required to conduct an annual evaluation of our internal controls over financial reporting and include a report of management on our internal controls in our annual reports on Form 10-K. If we are unable to continue to conclude that we have
effective internal controls over financial reporting or, if our independent auditor is unable to provide us with an attestation and an unqualified report as to the effectiveness of our internal controls over financial reporting, investors could lose
confidence in the reliability of our financial statements, which could result in a decrease in the value of our common stock.

We do not anticipate paying cash dividends, and accordingly stockholders must rely on stock appreciation for any return on their
investment in us.

We anticipate that we will retain our earnings, if any, for future growth and therefore do not
anticipate paying cash dividends in the future. As a result, only appreciation in the price of our common stock will provide a return to stockholders.



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Risks Related to Our Dependence on Third Parties

We may not be able to execute our business strategy if we are unable to enter into alliances with other companies that can provide
capabilities and funds for the development and commercialization of our drug candidates. If we are unsuccessful in forming or maintaining these alliances on favorable terms, our business may not succeed.

We have entered into a collaboration arrangement with Gilead for the development and commercialization of certain of our HCV compounds
involving NS4A antagonism. We have entered into a license agreement with GCAT for elvucitabine for the treatment of both HBV and HIV infection in mainland China, Hong Kong, and Taiwan. We may enter into additional collaborative arrangements in the
future. We are continuing partnering efforts for elvucitabine with regional companies and institutions, including those in South America, South Africa and elsewhere. We do not plan to clinically advance elvucitabine or ACH-702 independently. We also
may enter into alliances with major biotechnology or pharmaceutical companies to jointly develop other specific drug candidates and to jointly commercialize them if they are approved. In such alliances, we would expect our biotechnology or
pharmaceutical collaborators to provide substantial funding, as well as significant capabilities in clinical development, regulatory affairs, marketing and sales. We may not be successful in entering into any such alliances on favorable terms, if at
all. Even if we do succeed in securing such alliances, we may not be able to maintain them if, for example, development or approval of a drug candidate is delayed or sales of an approved drug are disappointing. Furthermore, any delay in entering
into collaboration agreements could delay the development and commercialization of our drug candidates and reduce their competitiveness even if they reach the market. Any such delay related to our collaborations could adversely affect our business.

If a collaborative partner terminates or fails to perform its obligations under agreements with us, the development and
commercialization of our drug candidates could be delayed or terminated.

If Gilead, GCAT or another future collaborative
partner does not devote sufficient time and resources to collaboration arrangements with us, we may not realize the potential commercial benefits of the arrangement, and our results of operations may be adversely affected. For example, in May 2009,
Gilead notified us that they do not intend to initiate clinical development of ACH-1095, and we subsequently amended our collaboration so that we may continue to develop ACH-1095, subject to certain rights of Gilead. Had we not come to an agreed
upon arrangement, the program would have been terminated, and our business may have been significantly harmed. Additionally, pursuant to the terms of the amended agreement, if Gilead elects not to exercise their right to opt in to ACH-1095
development, we will then become responsible for the development and commercialization of ACH-1095. Gilead maintains the right to terminate the continuing portions of the collaboration related to other NS4A antagonist compounds, and may exercise
that right at any time with requisite notice to us.

In addition, if any existing or future collaboration partner were to
breach or terminate its arrangements with us, the development and commercialization of the affected drug candidate could be delayed, curtailed or terminated because we may not have sufficient financial resources or capabilities to continue
development and commercialization of the drug candidate on our own. Under our collaboration agreement with Gilead, Gilead may terminate the collaboration for any reason at any time upon 30 days notice. If Gilead were to exercise this right, the
development and commercialization of our NS4A compounds for HCV infection would be adversely affected.

Much of the potential
revenue from our existing and future collaborations will consist of contingent payments, such as payments for achieving development milestones and royalties payable on sales of drugs developed. The milestone and royalty revenues that we may receive
under these collaborations will depend upon our collaborators ability to successfully develop, introduce, market and sell new products. In addition, our collaborators may decide to enter into arrangements with third parties to commercialize
products developed under our existing or future collaborations using our technologies, which could reduce the milestone and royalty revenue that we may receive, if any. In many cases we will not be involved in these processes and accordingly will
depend entirely on our collaborators. Our collaboration partners may fail to develop or effectively commercialize products using our products or technologies because they:



| |  |  | decide not to devote the necessary resources due to internal constraints, such as limited personnel with the requisite scientific expertise, limited
cash resources or specialized equipment limitations, or the belief that other drug development programs may have a higher likelihood of obtaining regulatory approval or may potentially generate a greater return on investment;
| | - |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | do not have sufficient resources necessary to carry the drug candidate through clinical development, regulatory approval and commercialization; or
| | - |  | --------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | cannot obtain the necessary regulatory approvals.
| | - |  | -------------------------------------------------



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In addition, a collaborator may decide to pursue a competitive drug candidate developed
outside of the collaboration. In particular, Gilead is currently developing other products for the treatment of chronic hepatitis C, and the results of its development efforts could affect its commitment to our drug candidates, including
Gileads desire to rejoin us in the future development of ACH-1095. If a collaboration partner fails to develop or effectively commercialize drug candidates or drugs for any of these reasons, we may not be able to replace the collaboration
partner with another partner to develop and commercialize a drug candidate or drugs under the terms of the collaboration. We may also be unable to obtain, on terms acceptable to us, a license from such collaboration partner to any of its
intellectual property that may be necessary or useful for us to continue to develop and commercialize a drug candidate.

We
rely on third parties to conduct our clinical trials, and those third parties may not perform satisfactorily, including failing to meet established deadlines for the completion of such trials.

We do not have the ability to independently conduct clinical trials for our drug candidates, and we rely on third parties such as
contract research organizations, medical institutions and clinical investigators to enroll qualified patients and conduct our clinical trials. Our reliance on these third parties for clinical development activities reduces our control over these
activities. These third-party contractors may not complete activities on schedule, or may not conduct our clinical trials in accordance with regulatory requirements or our trial design. To date, we believe our contract research organizations and
other similar entities with which we are working have performed well. However, if these third parties do not successfully carry out their contractual duties or meet expected deadlines, we may be required to replace them. Although we believe that
there are a number of other third-party contractors we could engage to continue these activities, it may result in a delay of the affected trial. Accordingly, our efforts to obtain regulatory approvals for and commercialize our drug candidates may
be delayed.

We currently depend on third-party manufacturers to produce our preclinical and clinical drug supplies and
intend to rely upon third-party manufacturers to produce commercial supplies of any approved drug candidates. If in the future we manufacture any of our drug candidates, we will be required to incur significant costs and devote significant efforts
to establish and maintain these capabilities.

We rely upon third parties to produce material for preclinical and clinical
testing purposes and intend to continue to do so in the future. We also expect to rely upon third parties to produce materials required for the commercial production of our drug candidates if we succeed in obtaining necessary regulatory approvals.
If we are unable to arrange for third-party manufacturing, or to do so on commercially reasonable terms, we may not be able to complete development of our drug candidates or market them. Reliance on third-party manufacturers entails risks to which
we would not be subject if we manufactured drug candidates ourselves, including reliance on the third party for regulatory compliance and quality assurance, the possibility of breach of the manufacturing agreement by the third party because of
factors beyond our control and the possibility of termination or nonrenewal of the agreement by the third party, based on its own business priorities, at a time that is costly or damaging to us. In addition, the FDA and other regulatory authorities
require that our drug candidates be manufactured according to current good manufacturing practice regulations. Any failure by us or our third-party manufacturers to comply with current good manufacturing practices and/or our failure to scale up our
manufacturing processes could lead to a delay in, or failure to obtain, regulatory approval of any of our drug candidates. In addition, such failure could be the basis for action by the FDA to withdraw approvals for drug candidates previously
granted to us and for other regulatory action.

To date, our third-party manufacturers have met our manufacturing
requirements, but we cannot be assured that they will continue to do so. Any performance failure on the part of our existing or future manufacturers could delay clinical development or regulatory approval of our drug candidates or commercialization
of any approved products. If for some reason our current contract manufacturers cannot perform as agreed, we may be required to replace them. Although we believe that there are a number of potential replacements given our manufacturing processes are
not manufacturer specific, we may incur added costs and delays in identifying and qualifying any such replacements. Furthermore, although we generally do not begin a clinical trial unless we believe we have a sufficient supply of a drug candidate to
complete the trial, any significant delay in the supply of a drug candidate for an ongoing trial due to the need to replace a third-party manufacturer could delay completion of the trial.

We may in the future elect to manufacture certain of our drug candidates in our own manufacturing facilities. If we do so, we will
require substantial additional funds and need to recruit qualified personnel in order to build or lease and operate any manufacturing facilities.



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Risks Related to Commercialization of Our Drug Candidates

If we are unable to establish sales and marketing capabilities or enter into agreements with third parties to market and sell our drug
candidates, we may not generate product revenue.

We have no commercial products, and we do not currently have an
organization for the sales and marketing of pharmaceutical products. In order to successfully commercialize any drugs that may be approved in the future by the FDA or comparable foreign regulatory authorities, we must build our sales and marketing
capabilities or make arrangements with third parties to perform these services. For certain drug candidates in selected indications where we believe that an approved product could be commercialized by a specialty North American sales force that
calls on a limited but focused group of physicians, we intend to commercialize these products ourselves. However, in therapeutic indications that require a large sales force selling to a large and diverse prescribing population and for markets
outside of North America, we plan to enter into arrangements with other companies for commercialization. For example, we have entered into an agreement with Gilead for the development and commercialization of certain of our HCV candidates involving
NS4A antagonism. If we are unable to establish adequate sales, marketing and distribution capabilities, whether independently or with third parties, we may not be able to generate product revenue and may not become profitable.

If we are unable to meet the operational, legal and financial challenges that we encounter with international partnerships, we may not
be able to grow our business.

We recently entered into an agreement with GCAT which grants GCAT, through its Chinese
joint venture with Tianjing Institute of Pharmaceutical Research, the right to clinically develop and commercialize elvucitabine in mainland China, Hong Kong and Taiwan. Conducting business in China exposes us to a variety of risks and uncertainties
that are unique to China. The economy of China has been transitioning from a planned economy to a market-oriented economy. Although in recent years the Chinese government has implemented measures emphasizing the utilization of market forces for
economic reform, the reduction of state ownership of productive assets and the establishment of sound corporate governance in business enterprises, a substantial portion of productive assets in China is still owned by the Chinese government. In
addition, the Chinese government continues to play a significant role in regulating industrial development. It also exercises significant control over Chinas economic growth through the allocation of resources, controlling payment of foreign
currency-denominated obligations, setting monetary policy and providing preferential treatment to particular industries or companies. Efforts by the Chinese government to slow the pace of growth of the Chinese economy could result in interruptions
of our development and commercialization efforts in China. In addition, the Chinese legal system is a civil law system based on written statutes. Unlike common law systems, it is a system in which decided legal cases have little precedential value.
In 1979, the Chinese government began to promulgate a comprehensive system of laws and regulations governing economic matters in general. Accordingly, we cannot predict the effect of future developments in the Chinese legal system, including the
promulgation of new laws, changes to existing laws or the interpretation or enforcement thereof, or the preemption of local regulations by national laws. Our development and commercialization efforts in China could be materially harmed by any
changes in the political, legal or economic climate in China or the inability to enforce applicable Chinese laws and regulations. If such commercialization efforts in China are materially harmed, our collaboration partner may not be able to develop
and commercialize elvucitabine in China and our elvucitabine business may not grow.

If physicians and patients do not
accept our future drugs, we may be unable to generate significant revenue, if any.

Even if ACH-1625, ACH-1095, ACH-2684,
ACH-2928, ACH-702, elvucitabine or any other drug candidates we may develop or acquire in the future obtain regulatory approval, they may not gain market acceptance among physicians, health care payors, patients and the medical community. Factors
that we believe could materially affect market acceptance of our product candidates include:



| |  |  | the timing of market introduction of competitive drugs;
| | - |  | -------------------------------------------------------



| |  |  | the demonstrated clinical safety and efficacy of our product candidates compared to other drugs;
| | - |  | ------------------------------------------------------------------------------------------------



| |  |  | the cost-effectiveness of our product candidates;
| | - |  | -------------------------------------------------



| |  |  | the availability of reimbursement from managed care plans, the government and other third-party payors;
| | - |  | -------------------------------------------------------------------------------------------------------



| |  |  | the convenience and ease of administration of our product candidates;
| | - |  | ---------------------------------------------------------------------



| |  |  | the existence, prevalence and severity of adverse side effects;
| | - |  | ---------------------------------------------------------------



| |  |  | other potential advantages of alternative treatment methods; and
| | - |  | ----------------------------------------------------------------



| |  |  | the effectiveness of marketing and distribution support.
| | - |  | --------------------------------------------------------

If our approved drugs fail to achieve market acceptance, we would not be able to generate significant revenue.



The development of directly acting antivirals (DAAs) to
treat HCV, and the potential changes in market dynamics that may result from their introduction for HCV therapy, may present additional risks beyond those inherent in drug development.

We are developing four DAA compounds, in three distinct classes, for treatment of chronic HCV infection. Other companies are also
developing DAAs in these classes, as well as other classes. The current standard of care for HCV infection includes immunomodulatory therapy with pegylated interferon and ribavirin. No DAAs are currently approved for treatment of chronic HCV
infection.

The development plans for our compounds include treatment regimens with our inhibitors in combination with the
current standard of care (pegylated interferon and ribavirin), our inhibitors with the current standard of care plus another DAA, or our inhibitors with one or more DAAs without concomitant interferon or ribavirin therapy. These development programs
carry all the risks inherent in drug development activities, including the risk that they will fail to show efficacy or acceptable safety. In addition, these development programs may also be subject to additional regulatory, commercial and
manufacturing risks that may be additional to the risks inherent in drug development activities.

Regulatory guidelines for
approval of DAA drugs for the treatment of chronic HCV infection are evolving in the United States, Europe, and other countries. We anticipate that regulatory guidelines and regulatory agency responses to our and our competitors development
programs will continue to change, resulting in the risk that our activities may not meet unanticipated new standards or requirements, which could lead to delay, additional expense, or potential failure of development activities.

Furthermore, even if we or our competitors successfully develop DAAs whose use improves the current standard of care, current
HCV-treating physicians, HCV patients, healthcare payers, and others may not readily accept or pay for such improvements or new treatments.

In addition, because development of DAAs is an emerging field, the delay or failure of a competitor attempting to develop therapeutics
that could have been combined with our product candidates or that are perceived to be similar to our product candidates could have a significant adverse effect on the commercial or regulatory environment for our product candidates or on the price of
our stock. Other companies developing DAAs have more advanced development programs than we do. Their success or failure to successfully conclude clinical development and obtain marketing approval could have a material adverse affect on our
development and commercialization plans and activities.



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If third-party payors do not adequately reimburse patients for any of our drug candidates
that are approved for marketing, they might not be purchased or used, and our revenues and profits will not develop or increase.

Our revenues and profits will depend significantly upon the availability of adequate reimbursement for the use of any approved drug
candidates from governmental and other third-party payors, both in the United States and in foreign markets. Reimbursement by a third party may depend upon a number of factors, including the third-party payors determination that use of a
product is:



| |  |  | a covered benefit under its health plan;
| | - |  | ----------------------------------------



| |  |  | safe, effective and medically necessary;
| | - |  | ----------------------------------------



| |  |  | appropriate for the specific patient;
| | - |  | -------------------------------------



| |  |  | cost effective; and
| | - |  | -------------------



| |  |  | neither experimental nor investigational.
| | - |  | -----------------------------------------

Obtaining reimbursement approval for a product from each third-party and government payor is a time-consuming and costly process that
could require us to provide supporting scientific, clinical and cost-effectiveness data for the use of any approved drugs to each payor. We may not be able to provide data sufficient to gain acceptance with respect to reimbursement. There also
exists substantial uncertainty concerning third-party reimbursement for the use of any drug candidate incorporating new technology, and even if determined eligible, coverage may be more limited than the purposes for which the drug is approved by the
FDA. Moreover, eligibility for coverage does not imply that any drug will be reimbursed in all cases or at a rate that allows us to make a profit or even cover our costs. Interim payments for new products, if applicable, may also be insufficient to
cover our costs and may not be made permanent. Reimbursement rates may vary according to the use of the drug and the clinical setting in which it is used, may be based on payments allowed for lower-cost products that are already reimbursed, may be
incorporated into existing payments for other products or services, and may reflect budgetary constraints and/or imperfections in Medicare or Medicaid data used to calculate these rates. Net prices for products may be reduced by mandatory discounts
or rebates required by government health care programs or by any future relaxation of laws that restrict imports of certain medical products from countries where they may be sold at lower prices than in the United States.

In the United States, at both the federal and state levels, the government regularly proposes legislation to reform health care and its
cost, and such proposals have received increasing political attention. Congress is considering legislation to reform the U.S. health care system by expanding health insurance coverage, reducing health care costs and making other changes. While
health care reform may increase the number of patients who have insurance coverage for the use of any approved drug candidate, it may also include changes that adversely affect reimbursement for approved drug candidates. In addition, there has been,
and we expect that there will continue to be, federal and state proposals to constrain expenditures for medical products and services, which may affect payments for any of our approved products. The Centers for Medicare and Medicaid Services
frequently change product descriptors, coverage policies, product and service codes, payment methodologies and reimbursement values. Third-party payors often follow Medicare coverage policy and payment limitations in setting their own reimbursement
rates and may have sufficient market power to demand significant price reductions. As a result of actions by these third-party payors, the health care industry is experiencing a trend toward containing or reducing costs through various means,
including lowering reimbursement rates, limiting therapeutic class coverage and negotiating reduced payment schedules with service providers for drug products.

Our inability to promptly obtain coverage and profitable reimbursement rates from government-funded and private payors for any approved
products could have a material adverse effect on our operating results and our overall financial condition.

Healthcare
reform measures, if implemented, could hinder or prevent our commercial success.

There have been, and likely will
continue to be, legislative and regulatory proposals at the federal and state levels directed at broadening the availability of healthcare and containing or lowering the cost of healthcare. We cannot predict the initiatives that may be adopted in
the future. The continuing efforts of the government, insurance companies, managed care organizations and other payors of healthcare services to contain or reduce costs of healthcare may adversely affect:



| |  |  | the demand for any drug products for which we may obtain regulatory approval;
| | - |  | -----------------------------------------------------------------------------



| |  |  | our ability to set a price that we believe is fair for our products;
| | - |  | --------------------------------------------------------------------



| |  |  | our ability to generate revenues and achieve or maintain profitability;
| | - |  | -----------------------------------------------------------------------



| |  |  | the level of taxes that we are required to pay; and
| | - |  | ---------------------------------------------------



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| |  |  | the availability of capital.
| | - |  | ----------------------------

Risks Related to Patents and Licenses

If we are unable to adequately protect our drug candidates, or if we infringe the rights of others, our ability to successfully
commercialize our drug candidates will be harmed.

We own or hold exclusive licenses to several U.S. issued patents and
U.S. pending provisional and non-provisional patent applications, as well as pending PCT applications and associated non-US patents and patent applications. Our success depends in part on our ability to obtain patent protection both in the United
States and in other countries for our drug candidates. Our ability to protect our drug candidates from unauthorized or infringing use by third parties depends in substantial part on our ability to obtain and maintain valid and enforceable patents.
Due to evolving legal standards relating to the patentability, validity and enforceability of patents covering pharmaceutical inventions and the scope of claims made under these patents, our ability to maintain, obtain and enforce patents is
uncertain and involves complex legal and factual questions. Accordingly, rights under any issued patents may not provide us with sufficient protection for our drug candidates or provide sufficient protection to afford us a commercial advantage
against competitive products or processes. In addition, we cannot guarantee that any patents will issue from any pending or future patent applications owned by or licensed to us. Even if patents have issued or will issue, we cannot guarantee that
the claims of these patents are or will be valid or enforceable or will provide us with any significant protection against competitive products or otherwise be commercially valuable to us. Patent applications in the United States are maintained in
confidence for up to 18 months after their filing. In some cases, however, patent applications remain confidential in the U.S. Patent and Trademark Office, which we refer to as the U.S. Patent Office, for the entire time prior to issuance as a U.S.
patent. Similarly, publication of discoveries in the scientific or patent literature often lag behind actual discoveries. Consequently, we cannot be certain that we or our licensors or co-owners were the first to invent, or the first to file patent
applications on, our drug candidates or their use as anti-infective drugs. In the event that a third party has also filed a U.S. patent application relating to our drug candidates or a similar invention, we may have to participate in interference
proceedings declared by the U.S. Patent Office to determine priority of invention in the United States. The costs of these proceedings could be substantial and it is possible that our efforts would be unsuccessful, resulting in a loss of our U.S.
patent position. Furthermore, we may not have identified all U.S. and foreign patents or published applications that affect our business either by blocking our ability to commercialize our drugs or by covering similar technologies that affect our
drug market.

The laws of some foreign jurisdictions do not protect intellectual property rights to the same extent as in the
United States and many companies have encountered significant difficulties in protecting and defending such rights in foreign jurisdictions. If we encounter such difficulties in protecting or are otherwise precluded from effectively protecting our
intellectual property rights in foreign jurisdictions, our business prospects could be substantially harmed.

We license
patent rights from third-party owners. If such owners do not properly maintain or enforce the patents underlying such licenses, our competitive position and business prospects will be harmed.

We are party to a number of licenses that give us rights to third-party intellectual property that is necessary or useful for our
business. In particular, we have obtained a sublicense from Vion Pharmaceuticals and a license from Emory University with respect to elvucitabine. We may enter into additional licenses for third-party intellectual property in the future. Our success
will depend in part on the ability of our licensors to obtain, maintain and enforce patent protection for their intellectual property, in particular, those patents to which we have secured exclusive rights. Our licensors may not successfully
prosecute the patent applications to which we are licensed. Even if patents issue in respect of these patent applications, our licensors may fail to maintain these patents, may determine not to pursue litigation against other companies that are
infringing these patents, or may pursue such litigation less aggressively than we would. In addition, our licensors may terminate their agreements with us in the event we breach the applicable license agreement and fail to cure the breach within a
specified period of time. Without protection for the intellectual property we license, other companies might be able to offer substantially identical products for sale, which could adversely affect our competitive business position and harm our
business prospects.

Litigation regarding patents, patent applications and other proprietary rights may be expensive and
time consuming. If we are involved in such litigation, it could cause delays in bringing drug candidates to market and harm our ability to operate.

Our success will depend in part on our ability to operate without infringing the proprietary rights of third parties. Although we are not
currently aware of any litigation or other proceedings or third-party claims of intellectual property infringement related to our drug candidates, the pharmaceutical industry is characterized by extensive litigation regarding patents and other
intellectual property rights. Other parties may obtain patents in the future and allege that the use of our technologies infringes these patent claims or that we are employing their proprietary technology without authorization. Likewise, third
parties may challenge or infringe upon our existing or future patents. Under our license agreements with Vion Pharmaceuticals we have the right, but not an



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obligation, to bring actions against an infringing third party. If we do not bring an action within a specified number of days, the licensor may bring an action against the infringing party.
Pursuant to our license agreement with Emory University and our research collaboration and license agreement with Gilead, Emory and Gilead have the primary right, but not an obligation, to bring actions against an infringing third party. However, if
Gilead or Emory elects not to bring an action, we may bring an action against the infringing party.

Proceedings involving our
patents or patent applications or those of others could result in adverse decisions regarding:



| |  |  | the patentability of our inventions relating to our drug candidates; and/or
| | - |  | ---------------------------------------------------------------------------



| |  |  | the enforceability, validity or scope of protection offered by our patents relating to our drug candidates.
| | - |  | -----------------------------------------------------------------------------------------------------------

Even if we are successful in these proceedings, we may incur substantial costs and divert management time and attention in pursuing these
proceedings, which could have a material adverse effect on us. If we are unable to avoid infringing the patent rights of others, we may be required to seek a license, defend an infringement action or challenge the validity of the patents in court.
Patent litigation is costly and time consuming. We may not have sufficient resources to bring these actions to a successful conclusion. In addition, if we do not obtain a license, develop or obtain non-infringing technology, fail to defend an
infringement action successfully or have infringed patents declared invalid, we may:



| |  |  | incur substantial monetary damages;
| | - |  | -----------------------------------



| |  |  | encounter significant delays in bringing our drug candidates to market; and/or
| | - |  | ------------------------------------------------------------------------------



| |  |  | be precluded from participating in the manufacture, use or sale of our drug candidates or methods of treatment requiring licenses.
| | - |  | ----------------------------------------------------------------------------------------------------------------------------------

Because of the relative weakness of the Chinese legal system in general, and the intellectual property
rights in particular, we may not be able to enforce intellectual property rights in China.

The legal regime protecting
intellectual property rights in China is weak. Because the Chinese legal system in general, and the intellectual property regime in particular, are relatively weak, it is often difficult to create and enforce intellectual property rights in China.
Accordingly, we may not be able to effectively protect our intellectual property rights in China under the GCAT agreement.

Confidentiality agreements with employees and others may not adequately prevent disclosure of trade secrets and other proprietary
information and may not adequately protect our intellectual property.

We rely on trade secrets to protect our technology,
especially where we do not believe patent protection is appropriate or obtainable. However, trade secrets are difficult to protect. In order to protect our proprietary technology and processes, we also rely in part on confidentiality and
intellectual property assignment agreements with our corporate partners, employees, consultants, outside scientific collaborators and sponsored researchers and other advisors. These agreements may not effectively prevent disclosure of confidential
information nor result in the effective assignment to us of intellectual property, and may not provide an adequate remedy in the event of unauthorized disclosure of confidential information or other breaches of the agreements. In addition, others
may independently discover our trade secrets and proprietary information, and in such case we could not assert any trade secret rights against such party. Enforcing a claim that a party illegally obtained and is using our trade secrets is difficult,
expensive and time consuming, and the outcome is unpredictable. In addition, courts outside the United States may be less willing to protect trade secrets. Costly and time-consuming litigation could be necessary to seek to enforce and determine the
scope of our proprietary rights, and failure to obtain or maintain trade secret protection could adversely affect our competitive business position.



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|ITEM 6. | EXHIBITS
|------- | --------



|     |  |                                                                                                                                                                                                                                                              
|---- |  | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|31.1 |  | Certification of President and Chief Executive Officer of Achillion Pharmaceuticals, Inc. pursuant to Rule 13a-14(a) promulgated under the Securities Exchange Act of 1934, as
amended.                                                                      
|     | 
|31.2 |  | Certification of Chief Financial Officer of Achillion Pharmaceuticals, Inc. pursuant to Rule 13a-14(a) promulgated under the Securities Exchange Act of 1934, as
amended.                                                                                    
|     | 
|32.1 |  | Certification of President and Chief Executive Officer of Achillion Pharmaceuticals, Inc. pursuant to Rule 13a-14(b) promulgated under the Securities Exchange Act of 1934, as
amended, and Section 1350 of Chapter 63 of Title 18 of the United States Code.
|     | 
|32.2 |  | Certification of Chief Financial Officer of Achillion Pharmaceuticals, Inc. pursuant to Rule 13a-14(b) promulgated under the Securities Exchange Act of 1934, as amended, and
Section 1350 of Chapter 63 of Title 18 of the United States Code.              



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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the Registrant has duly caused this Report to be signed on its
behalf by the undersigned, thereunto duly authorized.



|                      |  |  |  |                                                                     
|--------------------- |  |  |  | --------------------------------------------------------------------
|                      |  |  |  | ACHILLION PHARMACEUTICALS, INC.                                     
|                      |  | 
|Date: August 13, 2010 |  |  |  | /S/    MICHAEL D.
KISHBAUCH                                         
|                      |  |  |  | President and Chief Executive Officer
(Principal Executive Officer) 
|                      |  | 
|Date: August 13, 2010 |  |  |  | /S/    MARY KAY
FENTON                                              
|                      |  |  |  | Chief Financial Officer
(Principal Financial and Accounting Officer)



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EXHIBIT INDEX



|           |  |                                                                                                                                                                                                                                                              
|---------- |  | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|ExhibitNo. |  | Exhibit                                                                                                                                                                                                                                                      
|           | 
|31.1       |  | Certification of President and Chief Executive Officer of Achillion Pharmaceuticals, Inc. pursuant to Rule 13a-14(a) promulgated under the Securities Exchange Act of 1934, as
amended.                                                                      
|           | 
|31.2       |  | Certification of Chief Financial Officer of Achillion Pharmaceuticals, Inc. pursuant to Rule 13a-14(a) promulgated under the Securities Exchange Act of 1934, as
amended.                                                                                    
|           | 
|32.1       |  | Certification of President and Chief Executive Officer of Achillion Pharmaceuticals, Inc. pursuant to Rule 13a-14(b) promulgated under the Securities Exchange Act of 1934, as
amended, and Section 1350 of Chapter 63 of Title 18 of the United States Code.
|           | 
|32.2       |  | Certification of Chief Financial Officer of Achillion Pharmaceuticals, Inc. pursuant to Rule 13a-14(b) promulgated under the Securities Exchange Act of 1934, as amended, and
Section 1350 of Chapter 63 of Title 18 of the United States Code.              



42