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UNITED STATES SECURITIES AND EXCHANGE COMMISSION
 Washington, D.C. 20549
 Form 10-K
  þ
    
    ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
 For the fiscal year ended December 31, 2010
 or
 o
    
    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 000-49839
 Idenix Pharmaceuticals, Inc.
 (Exact Name of Registrant as Specified in its Charter)
 Delaware
    
    45-0478605(State or Other Jurisdiction of 
Incorporation or Organization)
    
    (I.R.S. Employer
Identification No.)60 Hampshire Street, 
Cambridge, Massachusetts
    
    02139(Zip Code)(Address of Principal Executive Offices)
 (617) 995-9800  (Registrants telephone number, including area code)   Securities registered pursuant to Section 12(b) of the Act:
 Common Stock, $0.001 par value
    
    The NASDAQ Global Market(Title of class)
    
    (Name of exchange on which registered)
 Securities registered pursuant to Section 12(g) of the Act:
 NONE
 Yes o No þ
 o þ
 þ o
 o o
 o
  Large accelerated filer o
    
    Accelerated filer þ
    
    Non-accelerated filer o
    
    Smaller reporting company o(Do not check if a smaller reporting company)
 o þ
   DOCUMENTS INCORPORATED BY REFERENCE




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Idenix Pharmaceuticals, Inc.
 Form 10-K
 TABLE OF CONTENTS
 PART IItem 1. Business
    
    
    4Item 1A. Risk Factors
    
    
    19Item 1B. Unresolved Staff Comments
    
    
    39Item 2. Properties
    
    
    39Item 3. Legal Proceedings
    
    
    39Item 4. [Removed and Reserved]
    
    
    39PART IIItem 5. Market for Registrants Common Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities
    
    
    39Item 6. Selected Consolidated Financial Data
    
    
    40Item 7. Managements Discussion and Analysis of Financial Condition and Results of Operations
    
    
    41Item 7A. Quantitative and Qualitative Disclosure About Market Risk
    
    
    52Item 8. Financial Statements and Supplementary Data
    
    
    52Item 9. Changes in and Disagreements With Accountants on Accounting and Financial Disclosure
    
    
    52Item 9A. Controls and Procedures
    
    
    53Item 9B. Other Information
    
    
    53PART IIIItem 10. Directors, Executive Officers and Corporate Governance
    
    
    54Item 11. Executive Compensation
    
    
    54Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters
    
    
    54Item 13. Certain Relationships, Related Transactions and Director Independence
    
    
    54Item 14. Principal Accountant Fees and Services
    
    
    54PART IVItem 15. Exhibits and Financial Statement Schedules
    
    
    55SIGNATURES
    
    
    81Exhibit Index
    
    
    82EX-10.60 Employment Letter, dated December 8, 2010, by and between the Registrant and Douglas L. Mayers, M.D.EX-10.61 Employment Letter, dated December 9, 2010, by and between the Registrant and David N. Standring, Ph.D.EX-10.62 Employment Letter, dated November 30, 2010, by and between the Registrant and Maria StahlExhibit 21.1EX-23.1 Consent of PricewaterhouseCoopers LLPEX-31.1 CEO Cert Section 302EX-31.2 CFO Cert Section 302EX-32.1 CEO Cert Section 906EX-32.2 CFO Cert Section 906
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CAUTIONARY STATEMENT REGARDING FORWARD-LOOKING STATEMENTS
     3




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PART I
 
 Item 1.
    
    Business
 Overview
  Business Highlights
  Combination DAA Strategy.
 Nucleoside/Nucleotide Polymerase Inhibitors.
 Protease Inhibitors.
 Non-Nucleoside Polymerase Inhibitors. 10
  4




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NS5A Inhibitors
    Novartis Collaboration
 ® ® ® ®
 Products and Drug Candidates
 Hepatitis C
 HCV Background
  Nucleoside/Nucleotide Polymerase Inhibitors.
 Protease Inhibitors.
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Non-Nucleoside Polymerase Inhibitors.
 NS5A Inhibitors
  Combination DAA Development
  Nucleoside/Nucleotide Polymerase Inhibitors Development
 in vitro
 10 10
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Protease Inhibitors Development
  10
   Non-Nucleoside Polymerase Inhibitors Development
   10 10
 NS5A Inhibitors Development
   7




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HIV
  Hepatitis B
 ® ® ® ®
 Antiviral Research
  Our Scientists
  Focused Compound Library
  Target Selection
  Screening
  Pharmacology, Preclinical Development and Lead Optimization
 in vitro in vivo in vivo in vitro in vivo
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Collaborations
 Novartis Collaboration
  
    
    the development and commercialization agreement, under which we
collaborate with Novartis to develop, manufacture and commercialize
our drug candidates which it licenses from us;
    
    the manufacturing and supply agreement, under which Novartis
manufactured for us the API for the clinical development and
commercial supply of drug candidates it licensed from us and the
finishing and packaging of licensed products for commercial sale;
    
    the stockholders agreement, which was subsequently amended and
restated in July 2004 in connection with the closing of our initial
public offering; and
    
    the stock purchase agreement, under which Novartis purchased
approximately 54% of our outstanding capital stock from our then
existing stockholders for $255.0 million in cash, with an additional
aggregate amount of up to $357.0 million contingently payable to these
stockholders if we achieve predetermined milestones with respect to
the development of specific HCV drug candidates, including
valopicitabine, which we ceased developing in July 2007, and prodrugs.
  Development and Commercialization Agreement
   ® ® ® ®
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® ®
       Manufacturing and Supply Agreement
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Stockholders Agreement
  
    
    granted Novartis, together with certain other holders of our common
stock, rights to cause us to register, under the Securities Act of
1933, as amended, such shares of common stock;
    
    agreed to use our reasonable best efforts to nominate for election as
directors at least two designees of Novartis for so long as Novartis
and its affiliates own at least 35% of our voting stock and at least
one designee of Novartis for so long as Novartis and its affiliates
own at least 19.4% of our voting stock; and
    
    granted Novartis approval rights over a number of corporate actions
that we or our subsidiaries may take as long as Novartis and its
affiliates continue to own at least 19.4% of our voting stock.
 Novartis Stock Subscription Rights
  Stock Purchase Agreement
   GlaxoSmithKline Collaboration
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
    
    consented to the sale by us of approximately 2.5 million shares of our common stock to GSK;
    
    approved our entering into the GSK license agreement;
    
    waived its rights to buy a pro rata portion of the shares of our common stock issued to GSK;
    
    approved our granting of registration rights to GSK and waived its rights to participate in such registration; and
    
    waived, until a certain time, its rights to request that we file a registration statement on Novartis behalf or
include shares of our common stock owned by Novartis in any such registration statement filed on behalf of GSK.
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Cooperative Laboratory Agreement
 University of Cagliari
   Research and Development Expenses
  Manufacturing
    Sales and Marketing
  Patents and Licenses
  Hepatitis C Patent Portfolio
 Flaviviridae
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Hepatitis B Patent Portfolio and Licenses
      ® ®
 HIV Patent Portfolio
   Competition
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® ®
 ® ® ® ®
  Pharmaceutical Pricing and Reimbursement
   Regulatory Matters
 ® ® ® ®
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FDA Requirements for Approval of Drug Products
  
    
    product seizures;
    
    voluntary or mandatory recalls;
    
    voluntary or mandatory patient and physician notification;
    
    withdrawal of product approvals;
    
    prohibitions against or restrictions on the marketing of our products, if approved for commercial sale;
    
    fines;
    
    restrictions on importation of our products;
    
    injunctions;
    
    debarment;
    
    civil and criminal penalties; and
    
    suspension of review and/or refusal to approve pending applications.
  in vitro
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Foreign Regulation of Drug Product Approval in Europe
   Centralized Procedure
   Foreign Regulation of Drug Product Approval in Asia
  Marketing Applications Format
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Hazardous Materials
  Employees
  Available Information
 www.idenix.com www.sec.gov
 Corporate Information
  
 Item 1A.
    
    Risk Factors
  Factors Related to Our Business
 The FDA placed one of our drug candidates, IDX184 on partial clinical hold and our business may be
adversely affected if we are not able to continue to pursue development of IDX184 or if we are
significantly delayed in developing IDX184.
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Our product candidates may exhibit undesirable side effects when used alone or in combination with
other approved pharmaceutical products or investigational agents, which may delay or preclude their
further development or regulatory approval, or limit their use if approved.
  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 will need additional capital to fund our operations, including the development, manufacture and
potential commercialization of our drug candidates. If we do not have or cannot raise additional
capital when needed, we will be unable to develop and ultimately commercialize our drug candidates
successfully.
 ® ®
  
    
    with respect to 761, GSK is able to continue clinical development of this drug candidate, following the clinical hold imposed by the
FDA in February 2011, such that we receive certain clinical development milestone payments within the next 24 months;
    
    with respect to our other drug candidates, Novartis exercises its option to license any such drug candidates, and we receive related
license fees, milestone payments and development expense reimbursement payments from Novartis; with respect to any of our drug
candidates not licensed by Novartis, we receive related license fees, milestone payments and development expense reimbursement
payments from third-parties;
    
    with respect to Tyzeka®/Sebivo®, whether the level of royalty payments received from Novartis is significant; and
    
    the terms of a development and commercialization agreement, if any, that we enter into with respect to our drug candidate, IDX184, for
the treatment of HCV. We are currently seeking a partner who will assist in the future development and commercialization of IDX184.
Our efforts to find a partner may be slowed because the FDA has placed this drug candidate on partial clinical hold as a result of
serious adverse events related to elevated liver function tests that were detected during post drug exposure safety visits following a
14-day drug-drug interaction study of a combination of IDX184 and IDX320 in healthy volunteers.
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
    
    the amount of revenue that we may be able to realize from commercialization and sale of drug candidates, if any,
which are approved by regulatory authorities;
    
    the scope and results of our preclinical studies and clinical trials;
    
    the progress of our current preclinical and clinical development programs for HCV;
    
    the cost of obtaining, maintaining and defending patents on our drug candidates and our processes;
    
    the cost, timing and outcome of regulatory reviews;
    
    any costs associated with changes in rules and regulations promulgated by the FDA related to the drug development
process and/or clinical trials;
    
    the commercial potential of our drug candidates;
    
    the rate of technological advances in our markets;
    
    the cost of acquiring or in-licensing new discovery compounds, technologies, drug candidates or other business assets;
    
    the magnitude of our general and administrative expenses;
    
    any costs related to litigation in which we may be involved or related to any claims made against us;
    
    any costs we may incur under current and future licensing arrangements; and
    
    the costs of commercializing and launching other products, if any, which are successfully developed and approved for
commercial sale by regulatory authorities.
    Our research and development efforts may not result in additional drug candidates being discovered
on anticipated timelines, which could limit our ability to generate revenues.
  Our failure to successfully acquire or develop and market additional drug candidates or approved
drugs would impair our ability to grow.
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Our investments are subject to general credit, liquidity, market and interest rate risks, which may
be exacerbated by the volatility in the United States credit markets.
  The commercial markets which we intend to enter are subject to intense competition. If we are
unable to compete effectively, our drug candidates may be rendered noncompetitive or obsolete.
  ® ®
  
    
    significantly greater financial, technical and human resources than we have and may be better
equipped to discover, develop, manufacture and commercialize products;
    
    more extensive experience in conducting preclinical studies and clinical trials, obtaining
regulatory approvals and manufacturing and marketing pharmaceutical products;
    
    products that have been approved or drug candidates that are in late-stage development; and
    
    collaborative arrangements in our target markets with leading companies and research institutions.
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® ®
  If we are not able to attract and retain key management and scientific personnel and advisors, we
may not successfully develop our drug candidates or achieve our other business objectives.
   Our business has a substantial risk of product liability claims. If we are unable to obtain or
maintain appropriate levels of insurance, a product liability claim against us could adversely
affect our business.
  ® ® ® ® ® ® ® ®
 Our insurance policies are expensive and protect us only from some business risks, which will leave
us exposed to significant, uninsured liabilities.
  If the estimates we make, and the assumptions on which we rely, in preparing our financial
statements prove inaccurate, our actual results may vary from those reflected in our projections
and accruals.
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If we fail to design and maintain an effective system of internal controls, we may not be able to
accurately report our financial results or prevent fraud. As a result, current and potential
stockholders could lose confidence in our financial reporting, which could harm our business and
the trading price of our common stock.
    Our business is subject to international economic, political and other risks that could negatively
affect our results of operations or financial position.
  
    
    changes in a specific countrys or regions political or economic conditions, including Western Europe, in particular;
    
    potential negative consequences from changes in tax laws affecting our ability to repatriate profits;
    
    difficulty in staffing and managing widespread operations;
    
    unfavorable labor regulations applicable to our European or other international operations;
    
    changes in foreign currency exchange rates; and
    
    the need to ensure compliance with the numerous regulatory and legal requirements applicable to our business in each
of these jurisdictions and to maintain an effective compliance program to ensure compliance.
  We may be required to relocate one of our principal research facilities, which could interrupt our
business activities and result in significant expense.
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Factors Related to Development, Clinical Testing and Regulatory Approval of Our Drug Candidates
 All of our drug candidates are in development. Our drug candidates remain subject to clinical
testing and regulatory approval. If we are unable to develop our drug candidates, we will not be
successful.
 ® ® ® ® ® ®
  
    
    offer therapeutic or other improvements over existing drugs;
    
    be proven safe and effective in clinical trials;
    
    meet applicable regulatory standards;
    
    be capable of being produced in commercial quantities at acceptable costs; or
    
    be successfully commercialized.
  If our clinical trials are not successful, we will not obtain regulatory approval for the
commercial sale of our drug candidates.
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
    
    discussions with the FDA or comparable foreign authorities regarding the scope or design of our clinical trials;
    
    delays in obtaining, or the inability to obtain, required approvals from, or suspensions or termination by, institutional review
boards or other governing entities at clinical sites selected for participation in our clinical trials;
    
    delays in enrolling participants into clinical trials;
    
    lower than anticipated retention of participants in clinical trials;
    
    insufficient supply or deficient quality of drug candidate materials or other materials necessary to conduct our clinical trials;
    
    serious or unexpected drug-related side effects experienced by participants in our clinical trials; or
    
    negative results of clinical trials.
  
    
    we may be unable to commence human clinical trials of any drug candidates;
    
    GSK may be unable to continue human clinical trials of 761 or commence human clinical trials of any
other licensed compound due to the clinical hold imposed by the FDA on 761 in February 2011;
    
    Novartis may choose not to license our drug candidates and we may not be able to enter into other
collaborative arrangements for any of our other drug candidates; or
    
    we may not have the financial resources to continue the research and development of our drug candidates.
 If our drug candidates fail to obtain United States and/or foreign regulatory approval, we and our
partners will be unable to commercialize our drug candidates.
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Our products will be subject to ongoing regulatory review even after approval to market such
products is obtained. If we or our partners fail to comply with applicable United States and
foreign regulations, we or our partners could lose approvals that we or our partners have been
granted and our business would be seriously harmed.
   If we or our partners fail to comply with ongoing regulatory requirements after receipt of approval
to commercialize a product, we or our partners may be subject to significant sanctions imposed by
the FDA, EMEA or other United States and foreign regulatory authorities.
  
    
    warning letters and other regulatory authority communications
objecting to matters such as promotional materials and requiring
corrective action such as revised communications to healthcare
practitioners;
    
    civil penalties;
    
    criminal penalties;
    
    injunctions;
    
    product seizure or detention;
    
    product recalls;
    
    total or partial suspension of manufacturing; and
    
    FDA refusal to review or approve pending new drug applications or
supplements to new drug applications for previously approved products
and/or similar rejections of marketing applications or supplements by
foreign regulatory authorities.
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If we do not comply with laws regulating the protection of the environment and health and human
safety, our business could be adversely affected.
  Growing availability of specialty pharmaceuticals may lead to increased focus of cost containment.
  Factors Related to Our Relationship with Novartis
 Novartis has substantial control over us and could delay or prevent a change in corporate control.
  
    
    the election of our directors;
    
    any amendment of our restated certificate of incorporation or amended and restated by-laws;
    
    the approval of mergers and other significant corporate transactions, including a sale of substantially all of our assets; or
    
    the defeat of any non-negotiated takeover attempt that might otherwise benefit our other stockholders.
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Novartis has the right to exercise control over certain corporate actions, strategic direction, our
research and development focus and other material decisions that may not otherwise require
stockholder approval as long as it holds at least 19.4% of our voting stock.
  
    
    the authorization or issuance of additional shares of our capital stock or the capital stock of our subsidiaries, except for a
limited number of specified issuances;
    
    any change or modification to the structure of our board of directors or a similar governing body of any of our subsidiaries;
    
    any amendment or modification to any of our organizational documents or those of our subsidiaries;
    
    the adoption of a three-year strategic plan;
    
    the adoption of an annual operating plan and budget, if there is no approved strategic plan;
    
    any decision that would result in a variance of total annual expenditures, capital or expense, in excess of 20% from the
approved three-year strategic plan;
    
    any decision that would result in a variance in excess of the greater of $10.0 million or 20% of our profit or loss target in
the strategic plan or annual operating plan;
    
    the acquisition of stock or assets of another entity that exceeds 10% of our consolidated net revenue, net income or net assets;
    
    the sale, lease, license or other disposition of any assets or business which exceeds 10% of our net revenue, net income or net
assets;
    
    the incurrence of any indebtedness by us or our subsidiaries for borrowed money in excess of $2.0 million;
    
    any material change in the nature of our business or that of any of our subsidiaries;
    
    any change in control of Idenix or any subsidiary; and
    
    any dissolution or liquidation of Idenix or any subsidiary, or the commencement by us or any subsidiary of any action under
applicable bankruptcy, insolvency, reorganization or liquidation laws.
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We currently depend on Novartis for a significant portion of our revenues, for the continuing
commercialization of Tyzeka ® /Sebivo ® and for support in the development of
drug candidates Novartis could license from us in the future. If our development and
commercialization agreement with Novartis terminates, our business, in particular, the development
of our drug candidates and the commercialization of any products that we successfully develop could
be harmed.
 ® ®
 ® ® ® ® ® ® ® ®
  Novartis has the option to license from us drug candidates we discover or, in some cases, acquire.
If Novartis does not exercise its option or disputes the adequacy of the notice provided by us
pertaining to the drug candidate, or after we provide notice, delays its decision to exercise such
option with respect to a drug candidate, our development, manufacture and/or commercialization of
such drug candidate may be substantially delayed or limited.
 ® ®
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If we breach any of the numerous representations and warranties we made to Novartis under the
development and commercialization agreement or the stock purchase agreement, Novartis has the right
to seek indemnification from us for damages it suffers as a result of such breach. These amounts
could be substantial.
   ® ®
 If we materially breach our obligations or covenants arising under the development and
commercialization agreement with Novartis, we may lose our rights to develop or commercialize our
drug candidates.
  If we issue capital stock, in certain situations, Novartis will be able to purchase shares at par
value to maintain its percentage ownership in Idenix and, if that occurs, this could cause
dilution. In addition, Novartis has the right, under specified circumstances, to purchase a pro
rata portion of other shares that we may issue.
  
    
    the date that Novartis and its affiliates own less than 19.4% of our voting stock; or
    
    the date that Novartis becomes obligated under the stock purchase agreement to make
the additional future contingent payments of $357.0 million to our stockholders who
sold shares to Novartis in May 2003.
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
    
    securities issuable in connection with any stock split, reverse stock split,
stock dividend or recapitalization that we undertake that affects all holders
of our common stock proportionately;
    
    shares that Novartis has the right to purchase at par value, as described above;
    
    shares of common stock issuable upon exercise of stock options and other awards
pursuant to our 1998 equity incentive plan; and
    
    securities issuable in connection with our acquisition of all the capital stock
or all or substantially all of the assets of another entity.
  If Novartis terminates or fails to perform its obligations under the development and
commercialization agreement, we may not be able to successfully commercialize our drug candidates
licensed to Novartis and the development and commercialization of our other drug candidates could
be delayed, curtailed or terminated.
 ® ®
  Novartis has the right to market and sell products that compete with the drug candidates and
products that we license to it and any competition by Novartis could have a material adverse effect
on our business.
  Factors Related to Our Dependence on Third-Parties Other Than Novartis
 If we seek to enter into collaboration agreements for any drug candidates other than those licensed
to Novartis and GSK and we are not successful in establishing such collaborations, we may not be
able to continue development of those drug candidates.
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
    
    we may be required to expend our own funds to advance the drug candidate to commercialization;
    
    revenue from product sales could be delayed; or
    
    we may elect not to develop or commercialize the drug candidate.
 Our license agreement with GSK is important to our business. The milestone payments and royalties
we could receive under our license agreement with GSK could be delayed, reduced or terminated if
GSK terminates or fails to perform its obligations under its agreement with us or if GSK is
unsuccessful in its sales efforts.
   Our collaborations with outside scientists may be subject to restriction and change.
  We have depended on third-party manufacturers to manufacture products for us. If in the future we
manufacture any of our products, we will be required to incur significant costs and devote
significant efforts to establish these capabilities.
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Factors Related to Patents and Licenses
 If we are unable to adequately protect our patents and licenses related to our drug candidates, or
if we infringe the rights of others, it may not be possible to successfully commercialize products
that we develop.
    ® ®
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® ®
    
    
    ownership of patents and patent applications;
    
    the patentability of our inventions relating to our products and drug candidates; and/or
    
    the enforceability, validity or scope of protection offered by our patents relating to our products and drug candidates.
     
    
    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.
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Confidentiality agreements with employees and others may not adequately prevent disclosure of trade
secrets and other proprietary information.
  If any of our agreements that grant us the exclusive right to make, use and sell our drug
candidates are terminated, we and/or our collaboration partners may be unable to develop or
commercialize our drug candidates.
 ® ® ® ®
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Factors Related to Our Common Stock
 Our common stock may have a volatile trading price and low trading volume.
  
    
    realization of license fees and achievement of milestones under our development and commercialization agreement with
Novartis;
    
    realization of license fees, achievement of preclinical and clinical milestones and sales thresholds under the GSK license
agreement;
    
    reductions in proceeds associated with Novartis right to maintain its percentage ownership of our voting stock when we
issue shares at a price below fair market value;
    
    adverse developments regarding the safety and efficacy of Tyzeka®/Sebivo® or our other drug candidates;
    
    the results of ongoing and planned clinical trials of our drug candidates;
    
    developments in the market with respect to competing products or more generally the treatment of HBV, HCV or HIV;
    
    the results of preclinical studies and planned clinical trials of our other discovery-stage programs;
    
    future sales of, and the trading volume in, our common stock;
    
    the timing and success of the launch of products, if any, we successfully develop;
    
    future royalty payments received by us associated with sales of Tyzeka®/Sebivo®;
    
    the entry into key agreements, including those related to the acquisition or in-licensing of new programs, or the
termination of key agreements;
    
    the results and timing of regulatory actions relating to the approval of our drug candidates, including any decision by the
regulatory authorities to place a clinical hold on our drug candidates;
    
    the initiation of, material developments in or conclusion of litigation to enforce or defend any of our intellectual
property rights;
    
    the initiation of, material developments in or conclusion of litigation to defend products liability claims;
    
    the failure of any of our drug candidates, if approved, to achieve commercial success;
    
    the results of clinical trials conducted by others on drugs that would compete with our drug candidates;
    
    issues in manufacturing our drug candidates or any approved products;
    
    the loss of key employees;
    
    adverse publicity related to our company, our products or our product candidates;
    
    changes in estimates or recommendations by securities analysts who cover our common stock;
    
    future financings through the issuance of equity or debt securities or otherwise;
    
    changes in the structure of health care payment systems;
    
    our cash position and period-to-period fluctuations in our financial results;
    
    general and industry-specific economic conditions; and
    
    the decision by Novartis to license a drug candidate that has completed a proof-of-concept clinical trial.
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We do not anticipate paying cash dividends, so you must rely on stock price appreciation for any
return on your investment.
  Sales of additional shares of our common stock could result in dilution to existing stockholders
and cause the price of our common stock to decline.
   An investment in our common stock may decline in value as a result of announcements of business
developments by us or our competitors.
  
    
    our collaboration with Novartis;
    
    our collaboration with GSK;
    
    the results of our clinical trials pertaining to any of our drug candidates;
    
    the results of discovery, preclinical studies and clinical trials by us or our competitors;
    
    the acquisition of technologies, drug candidates or products by us or our competitors;
    
    the development of new technologies, drug candidates or products by us or our competitors;
    
    regulatory actions with respect to our drug candidates or products or those of our competitors, including those
relating to clinical trials, such as clinical holds imposed by regulatory authorities, marketing authorizations,
pricing and reimbursement;
    
    the timing and success of launches of any product we successfully develop;
    
    future royalty payments received by us associated with sales of Tyzeka®/Sebivo®;
    
    the market acceptance of any products we successfully develop;
    
    significant changes to our existing business model;
    
    the initiation of, material developments in or conclusion of litigation to enforce or defend any of our
intellectual property rights; and
    
    significant acquisitions, strategic partnerships, joint ventures or capital commitments by us or our competitors.
   38




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##### Table of Contents



We could be subject to class action litigation due to stock price volatility, which, if such
litigation occurs, will distract our management and could result in substantial costs or large
judgments against us.
   
 Item 1B.
    
    Unresolved Staff Comments
  
 Item 2.
    
    Properties
  Approximate SquareProperty Location
    
    Feet
    
    Use
    
    Lease Expiration DateCambridge, MA
    
    36,513 sq. ft.
    
    Office Headquarters
    
    December 201339,014 sq. ft.
    
    Office and Laboratory
    
    December 2013Montpellier, France
    
    35,215 sq. ft.
    
    Office and Laboratory
    
    April 2017
  
 Item 3.
    
    Legal Proceedings
  
 Item 4.
    
    [Removed and Reserved]
 
 PART II
 
 Item 5.
    
    Market for Registrants Common Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities
 Market Information
  High
    
    
    Low2010First quarter
    
    $
    3.15
    
    
    $
    2.12Second quarter
    
    
    5.34
    
    
    
    2.80Third quarter
    
    
    6.11
    
    
    
    2.57Fourth quarter
    
    
    5.37
    
    
    
    3.072009First quarter
    
    $
    6.78
    
    
    $
    1.86Second quarter
    
    
    4.15
    
    
    
    3.00Third quarter
    
    
    5.45
    
    
    
    2.75Fourth quarter
    
    
    3.22
    
    
    
    1.81
  39




---



##### Table of Contents



Stockholders
  Dividends
  Repurchase of Securities
  
 Item 6.
    
    Selected Consolidated Financial Data
  Years Ended December 31,2010
    
    
    2009
    
    
    2008
    
    
    2007
    
    
    2006(In Thousands, Except per Share Data)Consolidated Statements of Operations Data:Total revenues
    
    $
    10,222
    
    
    $
    12,616
    
    
    $
    10,049
    
    
    $
    68,028
    
    
    $
    67,377Operating expenses:Cost of revenues
    
    
    2,765
    
    
    
    2,210
    
    
    
    1,745
    
    
    
    2,001
    
    
    
    62Research and development
    
    
    44,506
    
    
    
    41,867
    
    
    
    53,887
    
    
    
    85,839
    
    
    
    96,080General and administrative
    
    
    23,439
    
    
    
    21,467
    
    
    
    27,130
    
    
    
    63,348
    
    
    
    56,954Restructuring and impairment charges
    
    
    2,238
    
    
    
    1,506
    
    
    
    297
    
    
    
    8,744
    
    
    
    Total operating expenses
    
    
    72,948
    
    
    
    67,050
    
    
    
    83,059
    
    
    
    159,932
    
    
    
    153,096Loss from operations
    
    
    (62,726
    )
    
    
    (54,434
    )
    
    
    (73,010
    )
    
    
    (91,904
    )
    
    
    (85,719
    )Other income, net
    
    
    1,131
    
    
    
    1,266
    
    
    
    2,848
    
    
    
    6,135
    
    
    
    10,719Gain on sale of equity securities
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    3,500
    
    
    
    Income tax benefit (expense)
    
    
    40
    
    
    
    (51
    )
    
    
    (44
    )
    
    
    (246
    )
    
    
    (87
    )Net loss
    
    $
    (61,555
    )
    
    $
    (53,219
    )
    
    $
    (70,206
    )
    
    $
    (82,515
    )
    
    $
    (75,087
    )Basic and diluted net loss per common share
    
    $
    (0.87
    )
    
    $
    (0.87
    )
    
    $
    (1.24
    )
    
    $
    (1.47
    )
    
    $
    (1.34
    )Shares used in computing basic and diluted
net loss per common share
    
    
    70,715
    
    
    
    61,498
    
    
    
    56,403
    
    
    
    56,169
    
    
    
    56,005
 December 31,2010
    
    
    2009
    
    
    2008
    
    
    2007
    
    
    2006(In Thousands)Consolidated Balance Sheets Data:Cash and cash equivalents
    
    $
    46,115
    
    
    $
    46,519
    
    
    $
    41,509
    
    
    $
    48,260
    
    
    $
    55,892Working capital
    
    
    29,496
    
    
    
    33,236
    
    
    
    30,465
    
    
    
    72,985
    
    
    
    110,159Total assets
    
    
    69,884
    
    
    
    76,650
    
    
    
    79,780
    
    
    
    160,540
    
    
    
    228,465Deferred revenue
    
    
    2,623
    
    
    
    1,025
    
    
    
    
    
    
    
    
    
    
    
    Deferred revenue, related party
    
    
    3,036
    
    
    
    6,155
    
    
    
    5,965
    
    
    
    8,372
    
    
    
    13,490Deferred revenue, net of current portion
    
    
    40,340
    
    
    
    19,393
    
    
    
    4,272
    
    
    
    4,272
    
    
    
    4,272Deferred revenue, related party, net of current portion
    
    
    28,588
    
    
    
    30,776
    
    
    
    35,790
    
    
    
    41,861
    
    
    
    40,471Other long-term liabilities
    
    
    12,058
    
    
    
    13,590
    
    
    
    12,789
    
    
    
    14,835
    
    
    
    2,251Accumulated deficit
    
    
    (623,736
    )
    
    
    (562,181
    )
    
    
    (508,962
    )
    
    
    (438,756
    )
    
    
    (355,941
    )Total stockholders equity (deficit)
    
    
    (31,096
    )
    
    
    (5,453
    )
    
    
    7,353
    
    
    
    68,838
    
    
    
    142,025
  40




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##### Table of Contents



Item 7.
    
    Managements Discussion and Analysis of Financial Condition and Results of Operations
 Overview
  ® ® ® ®
   41




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##### Table of Contents



® ®
 Product/DrugIndication
    
    Candidates/Programs
    
    DescriptionHCV
    
    Nucleoside/Nucleotide Polymerase Inhibitors
(IDX184)
    
    Following a successfully completed proof-of-concept clinical
trial in treatment-naïve HCV genotype 1-infected patients, we
initiated a 14-day dose-ranging phase IIa clinical trial
evaluating IDX184 in combination with pegylated interferon and
ribavirin in treatment-naïve HCV genotype 1-infected patients.
This clinical trial was completed in the third quarter of 2010
and demonstrated that IDX184 is safe, well tolerated and has
potent HCV antiviral activity. We anticipate initiating a
phase IIb 12-week clinical trial in the second half of 2011.
Currently, our discovery efforts are concentrated on this
class of drugs to develop multiple follow-ons and novel
nucleoside/nucleotide drug candidates.Protease Inhibitors
(IDX320)
    
    In the first quarter of 2010, we completed a double-blind, placebo-controlled
phase I clinical study evaluating single and multiple ascending doses of
IDX320 in healthy volunteers. Based on the favorable safety and
pharmacokinetic data from the phase I clinical study, we initiated a three-day
proof-of-concept clinical trial in treatment-naïve HCV genotype 1-infected
patients, which was completed in the third quarter of 2010. This three-day
clinical trial demonstrated that IDX320 had potent HCV antiviral activity. The
IDX320 program was discontinued following the three serious adverse events of
liver injury in the 14-day phase I drug-drug interaction study of IDX184 and
IDX320, discussed above. We have follow-on
drug candidates in the protease inhibitor class that are
currently in preclinical development. We anticipate selecting
a clinical candidate with broad genotypic activity in 2011.Combination DAA Study
(IDX184 and IDX320)
    
    In the third quarter of 2010, we conducted a 14-day phase I
drug-drug interaction study of IDX184 and IDX320 in 20 healthy
volunteers. In September 2010, the FDA placed these drug
candidates on clinical hold due to three serious adverse
events of elevated liver function tests that were detected
during post drug exposure safety visits following this
drug-drug interaction study. We believe the hepatotoxicity
observed in this drug-drug interaction study was caused by
IDX320 and therefore discontinued the clinical development of
IDX320. In February 2011, the full clinical hold on IDX184 was
removed, which is described in more detail above.Non-Nucleoside Polymerase Inhibitor
(IDX375)
    
    In the first quarter of 2010, we submitted a clinical trial
application, or CTA, for a free acid form of IDX375. In the
fourth quarter of 2010, we completed a phase I clinical study
evaluating single and multiple doses of IDX375 in healthy
volunteers. Based on the favorable safety and pharmacokinetic
data from the phase I clinical study, we initiated a three-day
proof-of-concept clinical trial in treatment-naïve genotype
1-infected patients in the fourth quarter of 2010. After three
days of dosing with 100 mg, 200 mg and 400 mg of IDX375
administered twice a day, mean HCV viral load reductions were
1.3, 2.3 and 2.7 log10IU/mL, respectively.NS5A Inhibitors
    
    During 2010, we selected two lead candidates from our NS5A
discovery program. We anticipate selecting a clinical
candidate with broad genotypic activity and submitting an
investigational new drug, or IND, or a CTA in 2011, assuming
positive results from IND-enabling preclinical studies.HBV
    
    Tyzeka®/Sebivo®
(telbivudine)
(L-nucleoside)
    
    Novartis has worldwide development, commercialization and
manufacturing rights and obligations related to telbivudine
(Tyzeka®/Sebivo®).
We receive royalty payments equal to a percentage of net sales
of
Tyzeka®/Sebivo®.HIV
    
    Non-Nucleoside
Reverse Transcriptase Inhibitor
(IDX899 or 761)
    
    In February 2009, we granted GSK an exclusive worldwide
license to develop, manufacture and commercialize IDX899, now
known as 761. This drug candidate has progressed through
long-term chronic toxicology studies and drug-drug interaction
studies in healthy volunteers. In the fourth quarter of 2010,
GSK initiated a phase IIb clinical study of 761 in
HIV-infected patients. In February 2011, GSK informed us that
the FDA placed 761 on clinical hold. GSK has full
responsibility for the development of 761, including any
regulatory interactions.
   42




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##### Table of Contents



Disease
    
    
    
    Years Ended December 31,Indication
    
    Product/Drug Candidate
    
    2010
    
    
    2009
    
    
    2008(In Thousands)HCV
    
    Nucleotide Polymerase Inhibitors
    
    $
    8,412
    
    
    $
    6,052
    
    
    $
    7,004HCV
    
    Protease Inhibitors
    
    
    5,468
    
    
    
    2,665
    
    
    
    3,397HCV
    
    Non-Nucleoside Polymerase Inhibitor
    
    
    3,678
    
    
    
    3,537
    
    
    
    2,308HCV
    
    Combination DAA study
    
    
    747
    
    
    
    
    
    
    
    HCV
    
    Preclinical discovery program and other
    
    
    513
    
    
    
    517
    
    
    
    1,604HBV
    
    Telbivudine (Tyzeka®/Sebivo®) and other
    
    
    
    
    
    
    15
    
    
    
    286HIV
    
    Non-Nucleoside Reverse Transcriptase Inhibitor
    
    
    (26
    )
    
    
    (325
    )
    
    
    3,978$
    18,792
    
    
    $
    12,461
    
    
    $
    18,577
    ® ®
  Novartis Collaboration
  ® ®
   43




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##### Table of Contents



GlaxoSmithKline Collaboration
    Results of Operations
 Comparison of Years Ended December 31, 2010 and 2009
 Revenues
  Years Ended December 31,2010
    
    
    2009(In Thousands)Collaboration revenue  related party:License fee revenue
    
    $
    2,431
    
    
    $
    7,968Royalty revenue
    
    
    3,800
    
    
    
    3,704Reimbursement of research and development costs
    
    
    
    
    
    
    456,231
    
    
    
    11,717Other revenue:Collaboration revenue
    
    
    3,954
    
    
    
    854Government grants
    
    
    37
    
    
    
    45Total revenues
    
    $
    10,222
    
    
    $
    12,616
  
    
    license and other fees received from Novartis for the license of HBV and HCV drug
candidates, net of reductions for Novartis stock subscription rights, which is being
recognized over the development period of our licensed drug candidates;
    
    royalty payments associated with product sales of Tyzeka®/Sebivo® made by Novartis; and
    
    reimbursement by Novartis for expenses we incurred in connection with the development
and registration of our licensed products and drug candidates, net of certain
qualifying costs incurred by Novartis.
   44




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##### Table of Contents



Cost of Revenues
  Research and Development Expenses
    General and Administrative Expenses
   Restructuring Charges
   Other Income, Net
  Income Tax Benefit (Expense)
   45




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##### Table of Contents



Comparison of Years Ended December 31, 2009 and 2008
 Revenues
  Years Ended December 31,2009
    
    
    2008(In Thousands)Collaboration revenue  related party:License fee revenue
    
    $
    7,968
    
    
    $
    5,561Royalty revenue
    
    
    3,704
    
    
    
    2,885Reimbursement of research and development costs
    
    
    45
    
    
    
    1,36911,717
    
    
    
    9,815Other revenue:Collaboration revenue
    
    
    854
    
    
    
    Government grants and other revenue
    
    
    45
    
    
    
    234Total revenues
    
    $
    12,616
    
    
    $
    10,049
 ® ®
  Cost of Revenues
 ® ®
 Research and Development Expenses
  General and Administrative Expenses
  Restructuring Charges
  Other Income, Net
   46




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##### Table of Contents



Income Tax Expense
  Liquidity and Capital Resources
  
    
    license, milestone, royalty and other payments from Novartis;
    
    license, milestone and stock purchase payments from GSK;
    
    reimbursements from Novartis for costs we have incurred subsequent to May 8, 2003 in connection with the
development of Tyzeka®/Sebivo®, valtorcitabine and valopicitabine;
    
    sales of Tyzeka® in the United States through September 30, 2007;
    
    net proceeds from Sumitomo Pharmaceuticals Co., Ltd., or Sumitomo, for reimbursement of development costs;
    
    net proceeds from private placements of our convertible preferred stock;
    
    net proceeds from public or underwritten offerings in July 2004, October 2005, August 2009 and April 2010;
    
    net proceeds from private placements of our common stock concurrent with our 2004 and 2005 public offerings; and
    
    proceeds from the exercise of stock options granted pursuant to our equity compensation plans.
  ® ®
    47




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##### Table of Contents



Contractual Obligations and Commitments
  Payments Due by PeriodLess Than
    
    
    
    
    
    
    
    
    
    
    After 5Contractual Obligations
    
    Total
    
    
    1 Year
    
    
    1-3 Years
    
    
    4-5 Years
    
    
    Years(In Thousands)Operating leases
    
    $
    11,606
    
    
    $
    3,133
    
    
    $
    5,718
    
    
    $
    1,702
    
    
    $
    1,053Settlement payments and other agreements
    
    
    1,413
    
    
    
    1,249
    
    
    
    164
    
    
    
    
    
    
    
    Long-term obligations
    
    
    8,478
    
    
    
    
    
    
    
    1,199
    
    
    
    
    
    
    
    7,279Total contractual obligations
    
    $
    21,497
    
    
    $
    4,382
    
    
    $
    7,081
    
    
    $
    1,702
    
    
    $
    8,332
 ® ®
     48




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##### Table of Contents



Off-Balance Sheet Transactions
  Critical Accounting Policies and Estimates
   Revenue Recognition
 Revenue
Recognition in Financial Statements Revenue Recognition
   49




---



##### Table of Contents



Non-Refundable License Fee Payments
   Milestone Payments
   Collaboration Revenue  Related Party
    ® ® ® ®
  50




---



##### Table of Contents



Other Revenue
  Deferred Revenue
  Accrued Expenses
  Share-Based Compensation
     51




---



##### Table of Contents



Recent Accounting Pronouncements
 Multiple-Deliverable Revenue Arrangements
 Revenue Recognition  Milestone Method
 
 Item 7A.
    
    Quantitative and Qualitative Disclosure About Market Risk
 Interest Rate Risk
  Foreign Currency Exchange Rate Risk
 ®
 
 Item 8.
    
    Financial Statements and Supplementary Data
  
 Item 9.
    
    Changes in and Disagreements With Accountants on Accounting and Financial Disclosure
   52




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##### Table of Contents



Item 9A.
    
    Controls and Procedures
 Disclosure Controls and Procedures
 Evaluation of Disclosure Controls and Procedures
  Managements Annual Report on Internal Control Over Financial Reporting
  
    
    pertain to the maintenance of records that in reasonable detail
accurately and fairly reflect the transactions and dispositions of our
assets;
    
    provide reasonable assurance that transactions are recorded as
necessary to permit preparation of financial statements in accordance
with GAAP, and that our receipts and expenditures are being made only
in accordance with authorizations of our management and directors; and
    
    provide reasonable assurance regarding prevention or timely detection
of unauthorized acquisition, use or disposition of our assets that
could have a material effect on the financial statements.
  Internal Control-Integrated
Framework.
   Changes in Internal Control Over Financial Reporting
  
 Item 9B.
    
    Other Information
   53




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##### Table of Contents



PART III
  
 Item 10.
    
    Directors, Executive Officers and Corporate Governance
  Codes of Business Conduct
 www.idenix.com
 
 Item 11.
    
    Executive Compensation
   
 Item 12.
    
    Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters
  
 Item 13.
    
    Certain Relationships, Related Transactions and Director Independence
  
 Item 14.
    
    Principal Accountant Fees and Services
   54




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##### Table of Contents



PART IV
 
 Item 15.
    
    Exhibits and Financial Statement Schedules
 Financial Statements:
 PageReport of Independent Registered Public Accounting Firm
    
    
    56Consolidated Balance Sheets at December 31, 2010 and 2009
    
    
    57Consolidated Statements of Operations for the Years Ended December 31, 2010, 2009 and 2008
    
    
    58Consolidated Statements of Stockholders Equity (Deficit) and Comprehensive Loss for the
Years Ended December 31, 2010, 2009 and 2008
    
    
    59Consolidated Statements of Cash Flows for the Years Ended December 31, 2010, 2009 and 2008
    
    
    61Notes to the Consolidated Financial Statements
    
    
    62
 Financial Statement Schedules.
 Exhibits.
  55




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##### Table of Contents



REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM
  Internal Control  Integrated Framework
    
  56




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
 
 CONSOLIDATED BALANCE SHEETS  (IN THOUSANDS, EXCEPT SHARE DATA)
 December 31,2010
    
    
    2009ASSETSCurrent assets:Cash and cash equivalents
    
    $
    46,115
    
    
    $
    46,519Restricted cash
    
    
    411
    
    
    
    411Receivables from related party
    
    
    840
    
    
    
    1,049Other receivables
    
    
    
    
    
    
    1,505Other current assets
    
    
    2,124
    
    
    
    2,096Total current assets
    
    
    49,490
    
    
    
    51,580Intangible asset, net
    
    
    9,843
    
    
    
    11,069Property and equipment, net
    
    
    7,179
    
    
    
    10,091Restricted cash
    
    
    750
    
    
    
    750Marketable securities
    
    
    
    
    
    
    1,584Other assets
    
    
    2,622
    
    
    
    1,576Total assets
    
    $
    69,884
    
    
    $
    76,650LIABILITIES AND STOCKHOLDERS DEFICITCurrent liabilities:Accounts payable
    
    $
    2,558
    
    
    $
    1,941Accrued expenses
    
    
    11,472
    
    
    
    8,779Deferred revenue
    
    
    2,623
    
    
    
    1,025Deferred revenue, related party
    
    
    3,036
    
    
    
    6,155Other current liabilities
    
    
    305
    
    
    
    444Total current liabilities
    
    
    19,994
    
    
    
    18,344Other long-term liabilities
    
    
    12,058
    
    
    
    13,590Deferred revenue, net of current portion
    
    
    40,340
    
    
    
    19,393Deferred revenue, related party, net of current portion
    
    
    28,588
    
    
    
    30,776Total liabilities
    
    
    100,980
    
    
    
    82,103Commitments and contingencies (Note 15)Stockholders deficit:Common stock, $0.001 par value; 125,000,000 shares authorized at
December 31, 2010
and 2009; 73,091,514 and 66,365,976 shares issued and outstanding at
December 31, 2010 and 2009, respectively
    
    
    73
    
    
    
    66Additional paid-in capital
    
    
    591,884
    
    
    
    555,692Accumulated other comprehensive income
    
    
    683
    
    
    
    970Accumulated deficit
    
    
    (623,736
    )
    
    
    (562,181
    )Total stockholders deficit
    
    
    (31,096
    )
    
    
    (5,453
    )Total liabilities and stockholders deficit
    
    $
    69,884
    
    
    $
    76,650
   57




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
 
 CONSOLIDATED STATEMENTS OF OPERATIONS  (IN THOUSANDS, EXCEPT PER SHARE DATA)
 Years Ended December 31,2010
    
    
    2009
    
    
    2008Revenues:Collaboration revenue  related party
    
    $
    6,231
    
    
    $
    11,717
    
    
    $
    9,815Other revenue
    
    
    3,991
    
    
    
    899
    
    
    
    234Total revenues
    
    
    10,222
    
    
    
    12,616
    
    
    
    10,049Operating expenses:Cost of revenues
    
    
    2,765
    
    
    
    2,210
    
    
    
    1,745Research and development
    
    
    44,506
    
    
    
    41,867
    
    
    
    53,887General and administrative
    
    
    23,439
    
    
    
    21,467
    
    
    
    27,130Restructuring charges
    
    
    2,238
    
    
    
    1,506
    
    
    
    297Total operating expenses
    
    
    72,948
    
    
    
    67,050
    
    
    
    83,059Loss from operations
    
    
    (62,726
    )
    
    
    (54,434
    )
    
    
    (73,010
    )Other income, net
    
    
    1,131
    
    
    
    1,266
    
    
    
    2,848Loss before income taxes
    
    
    (61,595
    )
    
    
    (53,168
    )
    
    
    (70,162
    )Income tax benefit (expense)
    
    
    40
    
    
    
    (51
    )
    
    
    (44
    )Net loss
    
    $
    (61,555
    )
    
    $
    (53,219
    )
    
    $
    (70,206
    )Basic and diluted net loss per common share
    
    $
    (0.87
    )
    
    $
    (0.87
    )
    
    $
    (1.24
    )Shares used in computing basic and diluted net loss per common share
    
    
    70,715
    
    
    
    61,498
    
    
    
    56,403
   58




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
 
 CONSOLIDATED STATEMENTS OF STOCKHOLDERS EQUITY (DEFICIT) AND COMPREHENSIVE LOSS  DECEMBER 31, 2010, 2009 and 2008
 (IN THOUSANDS, EXCEPT SHARE DATA)
 AccumulatedAdditional
    
    
    Other
    
    
    
    
    
    
    TotalCommon Stock
    
    
    Paid-in
    
    
    Comprehensive
    
    
    Accumulated
    
    
    Stockholders
    
    
    ComprehensiveShares
    
    
    Amount
    
    
    Capital
    
    
    Income
    
    
    Deficit
    
    
    Equity (Deficit)
    
    
    LossBalance at December 31, 2007
    
    
    56,189,467
    
    
    $
    56
    
    
    $
    506,800
    
    
    $
    738
    
    
    $
    (438,756
    )
    
    $
    68,838Issuance of common stock upon exercise of
stock options
    
    
    339,067
    
    
    
    1
    
    
    
    729
    
    
    
    
    
    
    
    
    
    
    
    730
    
    
    
    Issuance of common stock with related party
    
    
    10,325
    
    
    
    
    
    
    
    35
    
    
    
    
    
    
    
    
    
    
    
    35
    
    
    
    Share-based compensation
    
    
    
    
    
    
    
    
    
    
    5,402
    
    
    
    
    
    
    
    
    
    
    
    5,402
    
    
    
    Antidilution shares contingently issuable to
related party
    
    
    
    
    
    
    
    
    
    
    2,917
    
    
    
    
    
    
    
    
    
    
    
    2,917
    
    
    
    Net loss
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (70,206
    )
    
    
    (70,206
    )
    
    $
    (70,206
    )Net change in unrealized holding loss on
marketable securities, net of tax
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    63
    
    
    
    
    
    
    
    63
    
    
    
    63Cumulative translation adjustment
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (426
    )
    
    
    
    
    
    
    (426
    )
    
    
    (426
    )Comprehensive loss
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    $
    (70,569
    )Balance at December 31, 2008
    
    
    56,538,859
    
    
    $
    57
    
    
    $
    515,883
    
    
    $
    375
    
    
    $
    (508,962
    )
    
    $
    7,353Issuance of common stock upon exercise of
stock options
    
    
    90,987
    
    
    
    
    
    
    
    150
    
    
    
    
    
    
    
    
    
    
    
    150
    
    
    
    Issuance of common stock with related party
    
    
    11,466
    
    
    
    
    
    
    
    28
    
    
    
    
    
    
    
    
    
    
    
    28
    
    
    
    Issuance of common stock to GlaxoSmithKline
    
    
    2,475,728
    
    
    
    2
    
    
    
    16,998
    
    
    
    
    
    
    
    
    
    
    
    17,000
    
    
    
    Issuance of common stock, net of offering
costs
    
    
    7,248,936
    
    
    
    7
    
    
    
    21,163
    
    
    
    
    
    
    
    
    
    
    
    21,170
    
    
    
    Share-based compensation
    
    
    
    
    
    
    
    
    
    
    4,614
    
    
    
    
    
    
    
    
    
    
    
    4,614
    
    
    
    Antidilution shares contingently issuable to
related party
    
    
    
    
    
    
    
    
    
    
    (3,144
    )
    
    
    
    
    
    
    
    
    
    
    (3,144
    )
    
    
    Net loss
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (53,219
    )
    
    
    (53,219
    )
    
    $
    (53,219
    )Net change in unrealized holding gain on
marketable securities, net of tax
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    31
    
    
    
    
    
    
    
    31
    
    
    
    31Cumulative translation adjustment
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    564
    
    
    
    
    
    
    
    564
    
    
    
    564Comprehensive loss
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    $
    (52,624
    )Balance at December 31, 2009
    
    
    66,365,976
    
    
    $
    66
    
    
    $
    555,692
    
    
    $
    970
    
    
    $
    (562,181
    )
    
    $
    (5,453
    )
   59




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
CONSOLIDATED STATEMENTS OF STOCKHOLDERS EQUITY (DEFICIT) AND COMPREHENSIVE LOSS  (CONTINUED)
DECEMBER 31, 2010, 2009 and 2008
(IN THOUSANDS, EXCEPT SHARE DATA)
 AccumulatedAdditional
    
    
    Other
    
    
    
    
    
    
    TotalCommon Stock
    
    
    Paid-in
    
    
    Comprehensive
    
    
    Accumulated
    
    
    Stockholders
    
    
    ComprehensiveShares
    
    
    Amount
    
    
    Capital
    
    
    Income
    
    
    Deficit
    
    
    Equity (Deficit)
    
    
    LossIssuance of common stock upon exercise of
stock options
    
    
    207,346
    
    
    
    
    
    
    
    494
    
    
    
    
    
    
    
    
    
    
    
    494
    
    
    
    Issuance of common stock with related party
    
    
    57,520
    
    
    
    
    
    
    
    145
    
    
    
    
    
    
    
    
    
    
    
    145
    
    
    
    Issuance of common stock, net of offering
costs
    
    
    6,460,672
    
    
    
    7
    
    
    
    26,259
    
    
    
    
    
    
    
    
    
    
    
    26,266
    
    
    
    Share-based compensation
    
    
    
    
    
    
    
    
    
    
    6,417
    
    
    
    
    
    
    
    
    
    
    
    6,417
    
    
    
    Antidilution shares contingently issuable to
related party
    
    
    
    
    
    
    
    
    
    
    2,877
    
    
    
    
    
    
    
    
    
    
    
    2,877
    
    
    
    Net loss
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (61,555
    )
    
    
    (61,555
    )
    
    $
    (61,555
    )Cumulative translation adjustment
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    (287
    )
    
    
    
    
    
    
    (287
    )
    
    
    (287
    )Comprehensive loss
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    
    $
    (61,842
    )Balance at December 31, 2010
    
    
    73,091,514
    
    
    $
    73
    
    
    $
    591,884
    
    
    $
    683
    
    
    $
    (623,736
    )
    
    $
    (31,096
    )
   60




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
 
 CONSOLIDATED STATEMENTS OF CASH FLOWS
 (IN THOUSANDS)
 Years Ended December 31,2010
    
    
    2009
    
    
    2008Cash flows from operating activities:Net loss
    
    $
    (61,555
    )
    
    $
    (53,219
    )
    
    $
    (70,206
    )Adjustments to reconcile net loss to net cash used in operating activities:Depreciation and amortization
    
    
    4,576
    
    
    
    5,186
    
    
    
    5,403Share-based compensation expense
    
    
    6,417
    
    
    
    4,614
    
    
    
    5,402Revenue adjustment for contingently issuable shares
    
    
    1,956
    
    
    
    (1,813
    )
    
    
    1,714Other
    
    
    161
    
    
    
    295
    
    
    
    1,166Changes in operating assets and liabilities:Receivables from related party
    
    
    209
    
    
    
    (155
    )
    
    
    10,302Other receivables
    
    
    1,610
    
    
    
    3,959
    
    
    
    (287
    )Other current assets
    
    
    (79
    )
    
    
    (599
    )
    
    
    2,001Other assets
    
    
    (1,112
    )
    
    
    (524
    )
    
    
    (279
    )Accounts payable
    
    
    620
    
    
    
    (1,927
    )
    
    
    (1,502
    )Accrued expenses and other current liabilities
    
    
    2,581
    
    
    
    (980
    )
    
    
    (7,173
    )Deferred revenue
    
    
    22,545
    
    
    
    16,146
    
    
    
    Deferred revenue, related party
    
    
    (4,387
    )
    
    
    (6,155
    )
    
    
    (7,274
    )Other liabilities
    
    
    (1,593
    )
    
    
    (788
    )
    
    
    (2,021
    )Net cash used in operating activities
    
    
    (28,051
    )
    
    
    (35,960
    )
    
    
    (62,754
    )Cash flows from investing activities:Purchases of property and equipment
    
    
    (727
    )
    
    
    (671
    )
    
    
    (2,250
    )Purchases of marketable securities
    
    
    
    
    
    
    
    
    
    
    (15,641
    )Sales and maturities of marketable securities
    
    
    1,476
    
    
    
    2,722
    
    
    
    73,211Net cash provided by investing activities
    
    
    749
    
    
    
    2,051
    
    
    
    55,320Cash flows from financing activities:Proceeds from exercise of common stock options
    
    
    494
    
    
    
    150
    
    
    
    730Proceeds from issuance of common stock to related party
    
    
    145
    
    
    
    28
    
    
    
    35Proceeds from issuance of common stock, net of offering costs
    
    
    26,266
    
    
    
    38,170
    
    
    
    Net cash provided by financing activities
    
    
    26,905
    
    
    
    38,348
    
    
    
    765Effect of changes in exchange rates on cash and cash equivalents
    
    
    (7
    )
    
    
    571
    
    
    
    (82
    )Net increase (decrease) in cash and cash equivalents
    
    
    (404
    )
    
    
    5,010
    
    
    
    (6,751
    )Cash and cash equivalents at beginning of year
    
    
    46,519
    
    
    
    41,509
    
    
    
    48,260Cash and cash equivalents at end of year
    
    $
    46,115
    
    
    $
    46,519
    
    
    $
    41,509Supplemental disclosure of cash flow information:Taxes paid
    
    $
    25
    
    
    $
    57
    
    
    $
    132Supplemental disclosure of non-cash investing and financing activities:Change in value of shares of common stock contingently issuable or issued
to related party
    
    
    2,877
    
    
    
    (3,144
    )
    
    
    2,917
   61




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
 
 NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS
 1. Organization
   ® ® ® ®
   ® ®
  62




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
 2. Summary of Significant Accounting Policies
  Principles of Consolidation
    Recent Accounting Pronouncements
 Multiple-Deliverable Revenue Arrangements,
 Revenue Recognition  Milestone Method
 Use of Estimates and Assumptions
  Cash and Cash Equivalents
   Concentration of Credit Risk
  ® ®
  63




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
 Marketable Securities
   Fair Value Measurements
   Intangible Asset
    December 31,2010
    
    
    2009(In Thousands)Beginning balance
    
    $
    11,069
    
    
    $
    12,387Amortization expense
    
    
    (1,226
    )
    
    
    (1,318
    )Ending balance
    
    $
    9,843
    
    
    $
    11,069
  64




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
  Property and Equipment
  Impairment of Long-Lived Assets
   Revenue Recognition
 Revenue Recognition in Financial Statements Revenue Recognition
  Non-Refundable License Fee Payments
   Milestone Payments
    65




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
 Collaboration Revenue  Related Party
   ® ® ® ®
 Other Revenue
   Deferred Revenue
   66




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
 Deferred Expenses
  Research and Development Expenses
  Patents
  Share-Based Compensation
  Foreign Currency
  Income Taxes
   Comprehensive Loss
  Net Loss per Common Share
   67




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
 Segment Reporting
  3. Novartis Relationship
 Overview
  ® ®
 ® ® ® ® ® ®
  ® ® ® ®
   68




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
 Stockholders Agreement
  Novartis Stock Subscription Rights
       69




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
 Manufacturing and Supply Agreement
  Product Sales Arrangement
 ® ®
 4. Net Loss per Common Share
  Years Ended December 31,2010
    
    
    2009
    
    
    2008(In Thousands, Except per Share Data)Basic and diluted net loss per common share:Net loss
    
    $
    (61,555
    )
    
    $
    (53,219
    )
    
    $
    (70,206
    )Basic and diluted weighted average number
of common shares
outstanding
    
    
    70,715
    
    
    
    61,498
    
    
    
    56,403Basic and diluted net loss per common share
    
    $
    (0.87
    )
    
    $
    (0.87
    )
    
    $
    (1.24
    )
  Years Ended December 31,2010
    
    
    2009
    
    
    2008(In Thousands)Options
    
    
    7,032
    
    
    
    5,560
    
    
    
    5,678Contingently issuable shares to related party
    
    
    1,735
    
    
    
    
    
    
    
    1,871
  70




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
 5. Marketable Securities and Fair Value Measurements
  December 31, 2010Amortized
    
    
    Gross Unrealized
    
    
    Gross UnrealizedCost
    
    
    Gains
    
    
    Losses
    
    
    Market Value(In Thousands)Type of security:Money market funds
    
    $
    17,719
    
    
    $
    
    
    
    $
    
    
    
    $
    17,719$
    17,719
    
    
    $
    
    
    
    $
    
    
    
    $
    17,719
 December 31, 2009Amortized
    
    
    Gross Unrealized
    
    
    Gross UnrealizedCost
    
    
    Gains
    
    
    Losses
    
    
    Market Value(In Thousands)Type of security:Money market funds
    
    $
    40,806
    
    
    $
    
    
    
    $
    
    
    
    $
    40,806Auction rate security
    
    
    1,584
    
    
    
    
    
    
    
    
    
    
    
    1,584$
    42,390
    
    
    $
    
    
    
    $
    
    
    
    $
    42,390
   December 31,2010
    
    
    2009(In Thousands)Beginning balance
    
    $
    1,584
    
    
    $
    1,710Purchases, sales and settlements
    
    
    (1,476
    )
    
    
    Total realized/unrealized losses recognized in earnings
    
    
    (108
    )
    
    
    (126
    )Ending balance
    
    $
    
    
    
    $
    1,584
   71




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
 6. Property and Equipment, Net
  EstimatedUseful Life
    
    December 31,(Years)
    
    2010
    
    
    2009(In Thousands)Scientific equipment
    
    7
    
    $
    6,740
    
    
    $
    8,243Computer equipment and software
    
    2
    
    
    4,021
    
    
    
    3,972Enterprise software
    
    5
    
    
    2,599
    
    
    
    2,599Office furniture and equipment
    
    5  7
    
    
    1,386
    
    
    
    1,546Leasehold improvements
    
    *
    
    
    10,287
    
    
    
    11,488Construction-in-progress
    
    
    
    
    94
    
    
    
    3625,127
    
    
    
    27,884Less  accumulated depreciation
    
    
    
    
    (17,948
    )
    
    
    (17,793
    )$
    7,179
    
    
    $
    10,091
 *
    
    Shorter of asset life or lease term  7. Accrued Expenses
  December 31,2010
    
    
    2009(In Thousands)Research and development contract costs
    
    $
    1,948
    
    
    $
    1,342Payroll and benefits
    
    
    3,232
    
    
    
    3,930Professional fees
    
    
    797
    
    
    
    647Short-term portion of accrued settlement payment
    
    
    1,086
    
    
    
    710Restructuring costs
    
    
    147
    
    
    
    416Severance payments
    
    
    2,297
    
    
    
    Other
    
    
    1,965
    
    
    
    1,734$
    11,472
    
    
    $
    8,779
  8. Restructuring Charges
    72




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
 9. Equity Incentive Plans and Share-Based Compensation
      Years Ended December 31,2010
    
    
    2009
    
    
    2008(In Thousands)Research and development
    
    $
    1,214
    
    
    $
    1,546
    
    
    $
    2,005General and administrative
    
    
    5,203
    
    
    
    3,068
    
    
    
    3,397Total share-based compensation
expense
    
    $
    6,417
    
    
    $
    4,614
    
    
    $
    5,402
   Years Ended December 31,2010
    
    
    2009
    
    
    2008Weighted average fair value of options
    
    $
    2.03
    
    
    $
    3.12
    
    
    $
    2.99Risk-free interest rate
    
    
    1.97
    %
    
    
    1.94
    %
    
    
    2.83
    %Expected dividend yield
    
    
    0
    %
    
    
    0
    %
    
    
    0
    %Expected option term (in years)
    
    
    5.1
    
    
    
    5.1
    
    
    
    5.1Expected volatility
    
    
    70.9
    %
    
    
    70.2
    %
    
    
    63.2
    %
   73




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
  Weighted
    
    
    WeightedAverage
    
    
    Average
    
    
    AggregateNumber of
    
    
    Exercise Price
    
    
    Remaining
    
    
    IntrinsicShares
    
    
    per Share
    
    
    Contractual Term
    
    
    Value(In Thousands)Options outstanding at December 31, 2009
    
    
    5,559,727
    
    
    $
    7.72Granted
    
    
    2,280,721
    
    
    $
    3.67Cancelled
    
    
    (601,366
    )
    
    $
    7.23Exercised
    
    
    (207,346
    )
    
    $
    2.38Options outstanding at December 31, 2010
    
    
    7,031,736
    
    
    $
    6.61
    
    
    
    5.13
    
    
    $
    4,958Options exercisable at December 31, 2010
    
    
    5,465,719
    
    
    $
    7.35
    
    
    
    4.11
    
    
    $
    3,184Options vested and expected to vest at
December 31, 2010
    
    
    6,832,069
    
    
    $
    6.69
    
    
    
    5.01
    
    
    $
    4,711
     10. Income Taxes
  Years Ended December 31,2010
    
    
    2009
    
    
    2008Federal statutory rate benefit
    
    
    (34
    )%
    
    
    (34
    )%
    
    
    (34
    )%State tax benefit, net of federal
expense (benefit)
    
    
    (2
    )
    
    
    2
    
    
    
    1Permanent items
    
    
    1
    
    
    
    (1
    )
    
    
    1Other
    
    
    1
    
    
    
    (3
    )
    
    
    Valuation allowance
    
    
    34
    
    
    
    36
    
    
    
    32Effective income tax rate
    
    
    0
    %
    
    
    0
    %
    
    
    0
    %
  74




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
  December 31,2010
    
    
    2009(In Thousands)Depreciation
    
    $
    1,672
    
    
    $
    1,340Development contracts
    
    
    1,233
    
    
    
    1,436Nonqualified stock options
    
    
    7,202
    
    
    
    5,450Deferred licensing income
    
    
    16,916
    
    
    
    13,020Accrued expenses and other
    
    
    2,669
    
    
    
    3,137Capitalized research costs
    
    
    58,661
    
    
    
    51,838Research and development credits
    
    
    9,632
    
    
    
    9,143Foreign tax credit carryforward
    
    
    877
    
    
    
    877Net operating carryforwards
    
    
    90,656
    
    
    
    82,063Valuation allowance
    
    
    (189,518
    )
    
    
    (168,304
    )Deferred tax asset
    
    $
    
    
    
    $
    
       11. Employee Benefit Plans
     75




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##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
 12. Related Party Transactions
 ® ®
 13. Segment Reporting
  December 31,2010
    
    
    2009(In Thousands)United States
    
    $
    5,301
    
    
    $
    7,346France
    
    
    1,878
    
    
    
    2,745$
    7,179
    
    
    $
    10,091
 14. Collaborative Agreements and License Agreements
  GlaxoSmithKline Collaboration
       76




---



##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
   University of Cagliari
    Sumitomo Pharmaceuticals Co., Ltd.
     77




---



##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
 15. Commitments and Contingencies
 Lease Arrangements
  OperatingYears Ending December 31,
    
    Leases(In Thousands)2011
    
    $
    3,1332012
    
    
    2,9212013
    
    
    2,7972014
    
    
    8572015
    
    
    8452016 and thereafter
    
    
    1,053Total
    
    $
    11,606
    Contingencies
 Hepatitis C Drug Candidates
   78




---



##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
  Hepatitis B Product
 ® ®
  Legal Contingency
  Other Legal Contingency
   79




---



##### Table of Contents



IDENIX PHARMACEUTICALS, INC.
NOTES TO THE CONSOLIDATED FINANCIAL STATEMENTS  CONTINUED
 Indemnification
   16. Quarterly Financial Data

 (Unaudited)
 First
    
    
    Second
    
    
    Third
    
    
    Fourth
    
    
    TotalQuarter
    
    
    Quarter
    
    
    Quarter
    
    
    Quarter
    
    
    Year(In Thousands, Except per Share Data)2010Total revenues
    
    $
    2,683
    
    
    $
    1,316
    
    
    $
    3,788
    
    
    $
    2,435
    
    
    $
    10,222Total operating expenses
    
    
    19,335
    
    
    
    17,915
    
    
    
    16,643
    
    
    
    19,055
    
    
    
    72,948Net loss
    
    
    (16,212
    )
    
    
    (16,256
    )
    
    
    (12,930
    )
    
    
    (16,157
    )
    
    
    (61,555
    )Basic and diluted net loss per common share
    
    
    (0.24
    )
    
    
    (0.23
    )
    
    
    (0.18
    )
    
    
    (0.22
    )
    
    
    (0.87
    )2009Total revenues
    
    $
    4,011
    
    
    $
    2,449
    
    
    $
    3,107
    
    
    $
    3,049
    
    
    $
    12,616Total operating expenses
    
    
    17,326
    
    
    
    18,755
    
    
    
    15,102
    
    
    
    15,867
    
    
    
    67,050Net loss
    
    
    (12,926
    )
    
    
    (16,314
    )
    
    
    (11,667
    )
    
    
    (12,312
    )
    
    
    (53,219
    )Basic and diluted net loss per common share
    
    
    (0.23
    )
    
    
    (0.28
    )
    
    
    (0.18
    )
    
    
    (0.19
    )
    
    
    (0.87
    )
  80




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##### Table of Contents



SIGNATURES
  IDENIX PHARMACEUTICALS, INC.Date: March 7, 2011
    /s/ Ronald C. Renaud, Jr.Ronald C. Renaud, Jr.President and Chief Executive Officer  Name
    
    Title
    
    Date/s/ Ronald C. Renaud, Jr.

Ronald C. Renaud, Jr.
    
    President and Chief Executive Officer and
Director (Principal Executive Officer)
    
    March 7, 2011/s/ Daniella Beckman

Daniella Beckman
    
    Interim Chief Financial Officer and Treasurer
(Principal Financial and Accounting Officer)
    
    March 7, 2011/s/ Charles Cramb

Charles Cramb
    
    Director
    
    March 7, 2011/s/ Wayne Hockmeyer

Wayne Hockmeyer
    
    Director
    
    March 7, 2011/s/ Thomas Hodgson

Thomas Hodgson
    
    Director
    
    March 7, 2011/s/ Tamar Howson

Tamar Howson
    
    Director
    
    March 7, 2011/s/ Robert Pelzer

Robert Pelzer
    
    Director
    
    March 7, 2011/s/ Denise Pollard-Knight

Denise Pollard-Knight
    
    Director
    
    March 7, 2011/s/ Anthony Rosenberg

Anthony Rosenberg
    
    Director
    
    March 7, 2011
  81




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##### Table of Contents



EXHIBIT INDEX
 Incorporated by Reference toExhibit


    
    
    
    
    Exhibit

    
    Filing
    
    SECNumber


    Description
    
    Form
    
    No.

    
    Date
    
    File NumberArticles of Incorporation and By-Laws3.1
    

    Restated Certificate of Incorporation of the Registrant
    
    S-1
    
    
    3.1
    
    
    12/15/2003
    
    333-1111573.2
    

    Certificate of Amendment of Restated Certificate of Incorporation
    
    10-Q for 6/30/2004
    
    
    3.1
    
    
    8/26/2004
    
    000-498393.3
    

    Certificate of Amendment of Restated Certificate of Incorporation
    
    10-K for 12/31/2005
    
    
    3.3
    
    
    3/16/2006
    
    000-498393.4
    

    Certificate of Amendment of Restated Certificate of Incorporation
    
    10-K for 12/31/2007
    
    
    3.4
    
    
    3/14/2008
    
    000-498393.5
    

    Amended and Restated By-Laws
    
    10-Q for 6/30/2004
    
    
    3.2
    
    
    8/26/2004
    
    000-498394.1
    

    Specimen Certificate evidencing the Common Stock, $.001 par value
    
    S-1 Amendment 2
    
    
    4.1
    
    
    1/27/2004
    
    333-111157Material contracts  real estate10.1
    

    Lease Agreement, dated as of October 15, 1998, by and between
Idenix (Massachusetts) Inc. and CambridgePark One Limited
Partnership, as amended by the First Amendment to Lease dated as
of September 1, 2001
    
    S-1
    
    
    10.2
    
    
    12/15/2003
    
    333-11115710.2
    

    Lease Agreement, dated as of August 22, 2001, by and between
Idenix (Massachusetts) Inc. and West Cambridge Sciences Park
    
    S-1
    
    
    10.3
    
    
    12/15/2003
    
    333-11115710.3
    

    Amended and Restated Lease of Premises at 60 Hampshire Street,
Cambridge, Massachusetts, dated as of October 28, 2003, by and
between Idenix (Massachusetts) Inc. and BHX, LLC, as trustee of
205 Broadway Realty Trust
    
    S-1
    
    
    10.4
    
    
    12/15/2003
    
    333-11115710.4
    

    Administrative Lease Hotel DEnterprises Cap Gamma dated April
18, 2005 by and among Idenix SARL, Societe DEquipment de la
Region Montpellieraine and the Communate DAgglomeration de
Montpellier (English Translation)
    
    8-K
    
    
    10.1
    
    
    4/20/2005
    
    000-49839
  82




---



##### Table of Contents



Incorporated by Reference toExhibit


    
    
    
    
    Exhibit

    
    Filing
    
    SECNumber


    Description
    
    Form
    
    No.

    
    Date
    
    File Number10.5
    +

    Offer of Sale Hotel
    
    8-K
    
    
    10.2
    
    
    4/20/2005
    
    000-4983910.6
    

    Joint Guarantee made as of December 15, 2005 between the
Registrant and Societe DEquipment de la Region
Montpellieraine
    
    8-K
    
    
    10.3
    
    
    4/20/2005
    
    000-4983910.7
    

    Indenture of Lease, dated June 8, 2005, by and between
the Registrant and One Kendall Square Associates LLC
    
    8-K
    
    
    10.1
    
    
    6/13/2005
    
    000-4983910.8
    

    First Amendment of Lease dated July 24, 2006 by and
between the Registrant and RB Kendall Fee, LLC
    
    10-Q for 6/30/2006
    
    
    10.3
    
    
    8/8/2006
    
    000-4983910.9
    

    Second Amendment of Lease dated September 7, 2006 by and
between the Registrant and RB Kendall Fee, LLC
    
    10-Q for 9/30/2006
    
    
    10.1
    
    
    11/8/2006
    
    000-4983910.10
    

    Third Amendment of Lease, dated July 23, 2009, between
RB Kendall Fee, LLC and the Registrant
    
    10-Q for 9/30/2009
    
    
    10.1
    
    
    10/29/2009
    
    000-4983910.11
    

    Fourth Amendment of Lease, dated June 29, 2010, between
RB Kendall Fee, LLC and the Registrant
    
    10-Q for 6/30/2010
    
    
    10.3
    
    
    7/27/2010
    
    000-49839Material contracts Novartis Pharma AG and GlaxoSmithKline10.12
    

    Letter Agreement, dated as of March 21, 2003, by and
between the Registrant and Novartis Pharma AG
    
    S-1
    
    
    10.28
    
    
    12/15/2003
    
    333-11115710.13
    

    Amendment No. 1 to Letter Agreement, dated on or about
January 28, 2009, by and between the Registrant and
Novartis Pharma AG
    
    8-K
    
    
    10.3
    
    
    2/6/2009
    
    000-4983910.14
    +

    Restated and Amended Cooperative Agreement dated as of
May 8, 2003, by among Idenix SARL and Le Centre National
de la Recherche Scientifique, LUniversite Montpellier
II and Novartis Pharma AG
    
    S-1
    
    
    10.14
    
    
    12/15/2003
    
    333-11115710.15
    

    Letter Agreement, dated May 8, 2003, by and among the
Registrant, Idenix SARL, Novartis Pharma AG and the
University of Cagliari, amending the Cooperative
Agreement and License Agreement
    
    S-1
    
    
    10.19
    
    
    12/15/2003
    
    333-111157
  83




---



##### Table of Contents



Incorporated by Reference toExhibit


    
    
    
    
    Exhibit

    
    Filing
    
    SECNumber


    Description
    
    Form
    
    No.

    
    Date
    
    File Number10.16
    +

    Development,
License and
Commercialization
Agreement, dated as
of May 8, 2003, by
and among the
Registrant, Idenix
(Cayman) Limited
and Novartis Pharma
AG, as amended on
April 30, 2004
    
    S-1 Amendment 3
    
    
    10.24
    
    
    7/6/2004
    
    333-11115710.17
    +

    Master
Manufacturing and
Supply Agreement,
dated as of May 8,
2003, by and
between Idenix
(Cayman) Limited
and Novartis Pharma
AG
    
    S-1
    
    
    10.25
    
    
    12/15/2003
    
    333-11115710.18
    +

    Second Amendment,
dated as of
December 21, 2004,
to the Development,
License and
Commercialization
Agreement, by and
among the
Registrant, Idenix
(Cayman) Limited
and Novartis Pharma
AG, as amended on
April 30, 2004
    
    10-K for 12/31/2004
    
    
    10.16
    
    
    3/17/2005
    
    000-4983910.19
    +

    Amendment No. 3 to
the Development,
License and
Commercialization
Agreement,
effective as of
February 27, 2006,
by and among the
Registrant, Idenix
(Cayman) Limited
and Novartis Pharma
AG
    
    10-K for 12/31/2005
    
    
    10.14
    
    
    3/16/2006
    
    000-4983910.20
    +

    Amendment No. 4 to
the Development,
License and
Commercialization
Agreement, dated as
of September 28,
2007, by and among
the Registrant,
Idenix (Cayman)
Limited and
Novartis Pharma AG
    
    10-Q for 9/30/2007
    
    
    10.1
    
    
    11/8/2007
    
    000-4983910.21
    

    Amendment No. 5 to
the Development
License and
Commercialization
Agreement, dated on
or about January
28, 2009, between
the Registrant,
Idenix (Cayman)
Limited and
Novartis Pharma AG
    
    8-K
    
    
    10.2
    
    
    2/6/2009
    
    000-4983910.22
    +

    Transition Services
Agreement, dated as
of September 28,
2007, by and among
the Registrant,
Idenix (Cayman)
Limited and
Novartis Pharma AG
    
    10-Q for 9/30/2007
    
    
    10.2
    
    
    11/8/2007
    
    000-49839
  84




---



##### Table of Contents



Incorporated by Reference toExhibit


    
    
    
    
    Exhibit

    
    Filing
    
    SECNumber


    Description
    
    Form
    
    No.

    
    Date
    
    File Number10.23
    

    Amended and Restated
Stockholders
Agreement, dated July
27, 2004, by and
among the Registrant,
Novartis and the
stockholders
identified on the
signature pages
thereto
    
    10-K for
12/31/2004
    
    
    10.20
    
    
    3/17/2005
    
    000-4983910.24
    

    Par Value Stock
Purchase Agreement,
dated July 27, 2004,
by and between the
Registrant and
Novartis Pharma AG
    
    10-K for
12/31/2004
    
    
    10.21
    
    
    3/17/2005
    
    000-4983910.25
    +

    Stock Purchase
Agreement, dated as
of March 21, 2003, by
and among the
Registrant, Novartis
and the stockholders
identified on the
signature pages
    
    S-1 Amendment 3
    
    
    10.27
    
    
    7/6/2004
    
    333-1111510.26
    

    Concurrent Private
Placement Stock
Purchase Agreement,
dated July 27, 2004,
by and between the
Registrant and
Novartis Pharma AG
    
    10-K for
12/31/2004
    
    
    10.22
    
    
    3/17/2005
    
    000-4983910.27
    +

    Commercial
Manufacturing
Agreement dated as of
June 22, 2006 by and
between the
Registrant and
Novartis Pharma AG
    
    10-Q for
6/30/2006
    
    
    10.1
    
    
    8/8/2006
    
    000-4983910.28
    +

    Packaging Agreement
dated as of June 22,
2006 by and between
the Registrant and
Novartis Pharma AG
    
    10-Q for
6/30/2006
    
    
    10.2
    
    
    8/8/2006
    
    000-4983910.29
    

    Stock Purchase
Agreement, dated
February 4, 2009,
between the
Registrant and
SmithKline Beecham
Corporate
    
    8-K
    
    
    10.1
    
    
    2/6/2009
    
    000-4983910.30
    +

    License Agreement,
dated February 4,
2009, between the
Registrant and
SmithKline Beecham
Corporate
    
    10-K for 12.31.2008
    
    
    10.28
    
    
    3/4/2009
    
    000-4983910.31
    +

    First Amendment of
License Agreement,
dated May 20, 2010,
between the
Registrant and ViiV
Healthcare Company,
successor to
SmithKline Beecham
Corporation
    
    10-Q for 6/30/2010
    
    
    10.2
    
    
    7/27/10
    
    000-49839University of Cagliari10.32
    +

    Cooperative Antiviral
Research Activity
Agreement (the
Cooperative
Agreement), dated
January 4, 1999, by
and between Idenix
SARL and the
University of
Cagliari
    
    S-1
    
    
    10.16
    
    
    12/15/2003
    
    333-111157
  85




---



##### Table of Contents



Incorporated by Reference toExhibit


    
    
    
    
    Exhibit

    
    Filing
    
    SECNumber


    Description
    
    Form
    
    No.

    
    Date
    
    File Number10.33
    +

    License Agreement,
dated as of December
14, 2000, between the
Registrant and the
University of Cagliari
    
    S-1
    
    
    10.17
    
    
    12/15/2003
    
    333-11115710.34
    +

    Letter Agreement, dated
April 10, 2002, by and
between Idenix SARL and
the University of
Cagliari, amending the
Cooperative Agreement
and License Agreement
    
    S-1
    
    
    10.18
    
    
    12/15/2003
    
    333-11115710.35
    +

    Agreement, dated June
30, 2004, by and among
the Registrant, Idenix
SARL and the University
of Cagliari
    
    S-1 Amendment 3
    
    
    10.18.1
    
    
    7/6/2004
    
    333-11115710.36
    

    Collaborative Activities
    
    S-1
    
    
    10.18.2
    
    
    7/6/2004
    
    333-11115710.37
    +

    Agreement, dated
October 24, 2005, by
and among the
Registrant, Idenix SARL
and the Universita
degli Studi di Cagliari
    
    10-Q for
9/30/2005
    
    
    10.1
    
    
    11/08/2005
    
    000-4983910.38
    +

    Amendment Agreement,
dated February 4, 2009,
by and among the
Registrant, Idenix
SARL, SmithKline
Beecham Corporate,
Universita degli Studi
di Cagliari and Paolo
LaColla
    
    10-K for
12/31/2008
    
    
    10.35
    
    
    3/4/2009
    
    000-49839Miscellaneous10.39
    

    License Agreement dated
as of June 20, 1998 by
and between the
Registrant and the UAB
Research Foundation, as
amended by that First
Amendment Agreement,
dated as of June 20,
1998, and by that
Second Amendment
Agreement, dated as of
July 16, 1999
    
    S-1 Amendment 2
    
    
    10.31
    
    
    6/1/2004
    
    333-11115710.40
    +

    Master Services
Agreement, dated
February 25, 2003, by
and between the
Registrant and
Quintiles, Inc.
    
    S-1
    
    
    10.21
    
    
    12/15/2003
    
    333-11115710.41
    

    Master Services
Agreement, dated May
27, 1999, between
Idenix (Massachusetts),
Inc. and Quintiles
Scotland Ltd
    
    S-1
    
    
    10.20
    
    
    12/15/2003
    
    333-111157
  86




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##### Table of Contents



Incorporated by Reference toExhibit


    
    
    
    
    Exhibit

    
    Filing
    
    SECNumber


    Description
    
    Form
    
    No.

    
    Date
    
    File Number10.42
    

    Multiproject
Development and
Supply Agreement,
dated as of
December 20, 2001,
by and among the
Registrant, Idenix
SARL and Clariant
Life Science
Molecules
(Missouri) Inc.
    
    S-1
    
    
    10.22
    
    
    12/15/2003
    
    333-11115710.43
    +

    Agreement, dated as
of May 1, 2003,
between Idenix
(Cayman Limited and
Microbiologica
Quimica E
Farmaceutica Ltda.
    
    S-1 Amendment 3
    
    
    10.23
    
    
    7/6/2004
    
    333-11115710.44
    

    Final Settlement
Agreement, dated
March 26, 2003, by
and between the
Registrant and
Sumitomo
Pharmaceuticals
Co., Ltd.
    
    S-1
    
    
    10.13
    
    
    12/15/2003
    
    333-11115710.45
    

    Settlement
Agreement, dated as
of May 28, 2004, by
and between the
Registrant,
Jean-Pierre
Sommadossi, the
University of
Alabama at
Birmingham and the
University of
Alabama Research
Foundation
    
    S-1 Amendment 2
    
    
    10.34
    
    
    6/1/2004
    
    333-11115710.46
    

    Settlement
Agreement,
effective June 1,
2008, by and among
the Registrant,
Jean-Pierre
Sommadossi, the
University of
Montpellier II, Le
Centre National de
la Recherche
Scientifique, the
Board of Trustees
of the University
of Alabama on
behalf of the
University of
Alabama at
Birmingham, the
University of
Alabama Research
Foundation and
Emory University
    
    8-K
    
    
    10.1
    
    
    8/5/2008
    
    000-4983910.47
    

    Master Service
Agreement, dated
April 1, 2008, by
and between the
Registrant and
Parexel
International LLC
    
    10-Q for
6/30/2008
    
    
    10.1
    
    
    8/7/2008
    
    000-4983910.48
    +

    Agreement, dated
December 3, 2008,
by and between the
Registrant and
Paolo LaColla
    
    10-K for
12/31/2008
    
    
    10.46
    
    
    3/4/2009
    
    000-49839
  87




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##### Table of Contents



Incorporated by Reference toExhibit


    
    
    
    
    Exhibit

    
    Filing
    
    SECNumber


    Description
    
    Form
    
    No.

    
    Date
    
    File Number10.49
    +

    Master Agreement for Clinical Trial Management
Services, dated September 16, 2009, between
Pharmaceutical Research Associates, Inc. and the
Registrant
    
    10-Q for
9/30/2009
    
    
    10.2+
    
    
    10/29/2009
    
    000-4983910.50
    

    Master Agreement for Clinical Research Services, dated
January 30, 2009, by and
between Registrant and
ACLIRES International, Ltd.
    
    10-K for 12/31/2009
    
    
    10.49
    
    
    3/9/2010
    
    000-49839Material contracts  management contracts and
compensatory plans10.51
    #

    Form of Incentive Stock Option Agreement for awards
granted pursuant to the 2005 Stock Incentive Plan, as
amended
    
    8-K
    
    
    10.2
    
    
    6/13/2005
    
    000-4983910.52
    #

    Form of Non-Statutory Stock Option Agreement for
awards granted pursuant to the 2005 Stock Incentive
Plan, as amended
    
    8-K
    
    
    10.3
    
    
    6/13/2005
    
    000-4983910.53
    #

    Form of Incentive Stock Option Agreement for awards
granted pursuant to the 2004 Stock Incentive Plan
    
    10-K for
12/31/2004
    
    
    10.28
    
    
    3/17/2005
    
    000-4983910.54
    #

    Form of Non-Statutory Stock Option Agreement for
awards granted pursuant to the 2004 Stock Incentive
Plan
    
    10-K for
12/31/2004
    
    
    10.29
    
    
    3/17/2005
    
    000-4983910.55
    #

    2005 Stock Incentive Plan, as amended
    
    10-Q for
6/30/2010
    
    
    10.1
    
    
    7/27/2010
    
    000-4983910.56
    #

    2004 Stock Incentive Plan
    
    S-1 Amendment 2
    
    
    10.32
    
    
    5/28/2004
    
    333-11115710.57
    #

    Amended and Restated 1998 Equity Incentive Plan
    
    S-1 Amendment 2
    
    
    10.1
    
    
    6/1/2004
    
    333-11115710.58
    #

    Separation and General Release Agreement, dated as of
December 23, 2010, by and between the Registrant and
Jean-Pierre Sommadossi
    
    8-K
    
    
    10.1
    
    
    12/30/2010
    
    000-4983910.59
    #

    Employment Letter, dated December 1, 2010, by and
between the Registrant and Ronald C. Renaud, Jr.
    
    8-K
    
    
    10.1
    
    
    12/6/2010
    
    000-4983910.60
    #

    Employment Letter, dated December 8, 2010, by and
between the Registrant and Douglas L. Mayers, M.D.
    
    *
  88




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##### Table of Contents



Incorporated by Reference toExhibit


    
    
    
    
    Exhibit
    
    Filing
    
    SECNumber


    Description
    
    Form
    
    No.
    
    Date
    
    File Number10.61
    #

    Employment Letter,
dated December 9,
2010, by and between
the Registrant and
David N. Standring,
PH.D.
    
    *10.62
    #

    Employment Letter,
dated November 30,
2010, by and between
the Registrant and
Maria Stahl
    
    *Additional Exhibits21.1
    

    Subsidiaries of the Company
    
    *23.1
    

    Consent of
PricewaterhouseCoopers
LLP, an independent
registered public
accounting firm
    
    *31.1
    

    Certification of Chief
Executive Officer
pursuant to Rule
13a-14(a)/15d-14(a) of
the Securities
Exchange Act of 1934,
as amended
    
    *31.2
    

    Certification of
Interim Chief
Financial Officer
pursuant to Rule
13a-14(a)/15d-14(a) of
the Securities
Exchange Act of 1934,
as amended
    
    *32.1
    

    Certification of Chief
Executive Officer
pursuant to 18 U.S.C.
§1350, as adopted
pursuant to Section
906 of the
Sarbanes-Oxley Act of
2002
    
    *32.2
    

    Certification of
Interim Chief
Financial Officer
pursuant to 18 U.S.C.
§1350, as adopted
pursuant to Section
906 of the
Sarbanes-Oxley Act of
2002
    
    *
 *
    
    Filed herewith#
    
    Management contract or compensatory plan or arrangement filed as an exhibit to this report
pursuant to Items 15(a) and 15(c) of Form 10-K+
    
    Confidential treatment requested as to certain portions, which portions have been separately
filed with the Securities and Exchange Commission  89