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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549





FORM 10-Q





(Mark One)

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

For the quarterly period ended March 31, 2009

or



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

For the transition period from              to

Commission File Number: 000-30039





ADOLOR CORPORATION

(Exact Name of Registrant as Specified in Its Charter)







|                                                               |  |                                        
|-------------------------------------------------------------- |  | ---------------------------------------
|Delaware                                                       |  | 31-1429198                             
|(State or Other Jurisdiction of Incorporation or Organization) |  | (I.R.S. Employer Identification Number)

700 Pennsylvania Drive

Exton, Pennsylvania 19341

(Address of Principal Executive Offices and Zip
Code)

484-595-1500

(Registrants Telephone Number, Including Area Code)

Not Applicable

(Former Name, Former Address and Former Fiscal Year, If Changed Since Last Report)





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

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



|                        |  |   |  |                           |  |  
|----------------------- |  | - |  | ------------------------- |  | -
|Large accelerated filer |  |  ̈ |  | Accelerated filer         |  | x
|                        |  |   | 
|Non-accelerated filer   |  |  ̈ |  | Smaller reporting company |  |  ̈

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

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of
Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes   ̈    No   ̈

Indicate the number of shares
outstanding of each class of the registrants common stock, as of the latest practicable date



|                                          |  |                                 
|----------------------------------------- |  | --------------------------------
|Class                                     |  | Outstanding as of April 15, 2009
|Common Stock, par value $0.0001 per share |  | 46,333,735 Shares               









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ADOLOR CORPORATION

FORM 10-Q

March 31, 2009

INDEX



|         |  |                                                                                       |  |         
|-------- |  | ------------------------------------------------------------------------------------- |  | --------
|         |  |                                                                                       |  | Page No.
|         |  | CAUTIONARY NOTE REGARDING FORWARD-LOOKING STATEMENTS                                  |  | ii      
|         |  |                                                                                      
|PART I.  |  | FINANCIAL INFORMATION                                                                 |  |         
|         |  |                                                                                      
|ITEM 1.  |  | Financial Statements (unaudited):                                                     |  |         
|         |  |                                                                                      
|         |  | Balance Sheets at March 31, 2009 and December 31, 2008                                |  | 1       
|         |  |                                                                                      
|         |  | Statements of Operations for the three months ended March 31, 2009 and 2008           |  | 2       
|         |  |                                                                                      
|         |  | Statement of Stockholders Equity for the three months ended March 31, 2009           |  | 3       
|         |  |                                                                                      
|         |  | Statements of Cash Flows for the three months ended March 31, 2009 and 2008           |  | 4       
|         |  |                                                                                      
|         |  | Notes to Financial Statements                                                         |  | 5       
|         |  |                                                                                      
|ITEM 2.  |  | Managements Discussion and Analysis of Financial Condition and Results of Operations |  | 10      
|         |  |                                                                                      
|ITEM 3.  |  | Quantitative and Qualitative Disclosures About Market Risk                            |  | 16      
|         |  |                                                                                      
|ITEM 4.  |  | Controls and Procedures                                                               |  | 16      
|         |  |                                                                                      
|PART II. |  | OTHER INFORMATION                                                                     |  |         
|         |  |                                                                                      
|ITEM 1.  |  | Legal Proceedings                                                                     |  | 17      
|         |  |                                                                                      
|ITEM 1A. |  | Risk Factors                                                                          |  | 17      
|         |  |                                                                                      
|ITEM 6.  |  | Exhibits                                                                              |  | 27      
|         |  |                                                                                      
|         |  | Signatures                                                                            |  | 28      



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CAUTIONARY NOTE REGARDING FORWARD-LOOKING STATEMENTS

In addition to historical facts or statements of current condition, this report and the documents into which this report is and will be incorporated
contain forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended. Forward-looking statements contained in this report or
incorporated herein by reference constitute our expectations or forecasts of future events as of the date this report was filed with the Securities and Exchange Commission and are not statements of historical fact. You can identify these statements
by the fact that they do not relate strictly to historical or current facts. Such statements may include words such as anticipate, will, estimate, expect, project, intend,
should, plan, believe, hope and other words and terms of similar meaning in connection with any discussion of, among other things, sales, future operating or financial performance, strategic
initiatives and business strategies, regulatory or competitive environments, our intellectual property and product development. In particular, these forward-looking statements include, among others, statements about:



| |  |  | our dependence on sales of ENTEREG® (alvimopan) in
the United States and the commercial prospects and future marketing efforts for this product;
| | - |  | ------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | our anticipated scientific progress in our research programs and our development of potential pharmaceutical products, including our ongoing or planned clinical
trials, the status, timing, costs and results of such trials, the ability to secure regulatory approval for our product candidates and the likelihood or timing of revenues from these products, if any;
| | - |  | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | the scope and duration of our intellectual property protection for our products and product candidates, our ability to adequately protect our technologies and
enforce our intellectual property rights and the future expiration of patent and/or regulatory exclusivity on alvimopan;
| | - |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | our anticipated operating losses and cash requirements, projections regarding the levels of our cash, cash equivalents and investments and our ability to raise
additional funds in light of our current and projected level of operations; and
| | - |  | -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | other statements regarding matters that are not historical facts or statements of current condition.
| | - |  | ----------------------------------------------------------------------------------------------------

Any or all of our forward-looking statements in this report and in the documents to which we have referred you may turn out to be wrong. They can be
affected by inaccurate assumptions we might make or by known or unknown risks and uncertainties. Therefore, you should not place undue reliance on any such forward-looking statements. The factors that could cause actual results to differ from those
expressed or implied by our forward-looking statements include, among others:



| |  |  | the acceptance of ENTEREG by hospitals, physicians and patients in the marketplace;
| | - |  | -----------------------------------------------------------------------------------



| |  |  | scientific or regulatory setbacks with respect to research programs, clinical trials, manufacturing activities or commercial activities;
| | - |  | ----------------------------------------------------------------------------------------------------------------------------------------



| |  |  | the timing and unpredictability of regulatory actions;
| | - |  | ------------------------------------------------------



| |  |  | our ability to develop and launch new products effectively;
| | - |  | -----------------------------------------------------------



| |  |  | unanticipated cash requirements to support current operations, to expand our business or for capital expenditures;
| | - |  | ------------------------------------------------------------------------------------------------------------------



| |  |  | the inability to adequately protect our key intellectual property rights;
| | - |  | -------------------------------------------------------------------------



| |  |  | the loss of key management or scientific personnel;
| | - |  | ---------------------------------------------------



| |  |  | the activities of our competitors;
| | - |  | ----------------------------------



| |  |  | regulatory, legal or other setbacks with respect to our operations or business;
| | - |  | -------------------------------------------------------------------------------



| |  |  | market conditions in the capital markets and the biopharmaceutical industry that make raising capital or consummating acquisitions difficult, expensive or both; and
| | - |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | enactment of new government laws, regulations, court decisions, regulatory interpretations or other initiatives that are adverse to us or our interests.
| | - |  | --------------------------------------------------------------------------------------------------------------------------------------------------------



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We do not intend to update publicly any forward-looking statement, whether as a result of new
information, future events or otherwise, except as required by law. We discuss in more detail the risks that we anticipate in Part II, Item 1A of this report. This discussion is permitted by the Private Securities Litigation Reform Act of 1995.



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##### Table of Contents

ADOLOR CORPORATION

Balance Sheets

(Unaudited)



|                                                                                                                                                |  |               |              |   |                  |   |              |  
|----------------------------------------------------------------------------------------------------------------------------------------------- |  | ------------- | ------------ | - | ---------------- | - | ------------ | -
|                                                                                                                                                |  | March 31,2009 |              |   | December 31,2008 |  
|Assets                                                                                                                                          |  |               |              |   |                  |   |              |  
|Current assets:                                                                                                                                 |  |               |              |   |                  |   |              |  
|Cash and cash equivalents                                                                                                                       |  | $             | 17,155,618   |   |                  | $ | 7,535,146    |  
|Short-term investments                                                                                                                          |  |               | 107,516,511  |   |                  |   | 124,375,060  |  
|Accounts receivable                                                                                                                             |  |               | 1,359,551    |   |                  |   | 3,588,935    |  
|Inventory                                                                                                                                       |  |               | 144,390      |   |                  |   |             |  
|Prepaid expenses and other current assets                                                                                                       |  |               | 4,170,828    |   |                  |   | 4,348,209    |  
|                                                                                                                                                |  |               |              |   |                  |   |              |  
|Total current assets                                                                                                                            |  |               | 130,346,898  |   |                  |   | 139,847,350  |  
|Equipment and leasehold improvements, net                                                                                                       |  |               | 4,245,038    |   |                  |   | 4,466,803    |  
|Other assets                                                                                                                                    |  |               | 119,413      |   |                  |   | 112,414      |  
|                                                                                                                                                |  |               |              |   |                  |   |              |  
|Total assets                                                                                                                                    |  | $             | 134,711,349  |   |                  | $ | 144,426,567  |  
|                                                                                                                                                |  |               |              |   |                  |   |              |  
|Liabilities and Stockholders Equity                                                                                                            |  |               |              |   |                  |   |              |  
|Current liabilities:                                                                                                                            |  |               |              |   |                  |   |              |  
|Accounts payable                                                                                                                                |  | $             | 2,248,182    |   |                  | $ | 2,310,330    |  
|Accrued expenses                                                                                                                                |  |               | 8,411,245    |   |                  |   | 10,941,059   |  
|Customer deposits                                                                                                                               |  |               | 651,840      |   |                  |   | 274,425      |  
|Deferred revenue and rent  current                                                                                                             |  |               | 13,338,404   |   |                  |   | 14,071,511   |  
|                                                                                                                                                |  |               |              |   |                  |   |              |  
|Total current liabilities                                                                                                                       |  |               | 24,649,671   |   |                  |   | 27,597,325   |  
|Deferred revenue and rent  non-current                                                                                                         |  |               | 33,907,029   |   |                  |   | 28,207,240   |  
|Other liabilities                                                                                                                               |  |               | 3,040        |   |                  |   | 3,440        |  
|                                                                                                                                                |  |               |              |   |                  |   |              |  
|Total liabilities                                                                                                                               |  |               | 58,559,740   |   |                  |   | 55,808,005   |  
|                                                                                                                                                |  |               |              |   |                  |   |              |  
|Contingencies (Note 8)                                                                                                                          |  |               |              |   |                  |   |              |  
|                                                                                                                                                |  |              
|Stockholders equity:                                                                                                                           |  |               |              |   |                  |   |              |  
|Series A Junior Participating preferred stock, $0.01 par value; 35,000 shares authorized; none issued and outstanding                           |  |               |             |   |                  |   |             |  
|Preferred stock, $0.01 par value; 1,000,000 shares authorized; none issued and outstanding                                                      |  |               |             |   |                  |   |             |  
|Common stock, $0.0001 par value; 99,000,000 shares authorized; 46,333,735 shares issued and outstanding at March 31, 2009 and
December 31, 2008 |  |               | 4,633        |   |                  |   | 4,633        |  
|Additional paid-in capital                                                                                                                      |  |               | 544,142,986  |   |                  |   | 543,009,215  |  
|Unrealized gains on available for sale securities                                                                                               |  |               | 258,073      |   |                  |   | 671,457      |  
|Accumulated deficit                                                                                                                             |  |               | (468,254,083 | ) |                  |   | (455,066,743 | )
|                                                                                                                                                |  |               |              |   |                  |   |              |  
|Total stockholders equity                                                                                                                      |  |               | 76,151,609   |   |                  |   | 88,618,562   |  
|                                                                                                                                                |  |               |              |   |                  |   |              |  
|Total liabilities and stockholders equity                                                                                                      |  | $             | 134,711,349  |   |                  | $ | 144,426,567  |  
|                                                                                                                                                |  |               |              |   |                  |   |              |  

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



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ADOLOR CORPORATION

Statements of Operations

(Unaudited)



|                                                              |  |                              |             |   |      |   |             |  
|------------------------------------------------------------- |  | ---------------------------- | ----------- | - | ---- | - | ----------- | -
|                                                              |  | Three Months Ended March 31, |            
|                                                              |  | 2009                         |             |   | 2008 |  
|Revenues:                                                     |  |                              |             |   |      |   |             |  
|Product sales, net                                            |  | $                            | 1,432,183   |   |      | $ |            |  
|Contract revenues                                             |  |                              | 5,247,477   |   |      |   | 6,211,024   |  
|                                                              |  |                              |             |   |      |   |             |  
|Total revenues, net                                           |  |                              | 6,679,660   |   |      |   | 6,211,024   |  
|                                                              |  |                              |             |   |      |   |             |  
|                                                              |  |                             
|Operating expenses incurred:                                  |  |                              |             |   |      |   |             |  
|Cost of product sales                                         |  |                              | 153,304     |   |      |   |            |  
|Research and development                                      |  |                              | 12,322,623  |   |      |   | 11,421,072  |  
|Selling, general and administrative                           |  |                              | 7,877,674   |   |      |   | 5,548,530   |  
|                                                              |  |                              |             |   |      |   |             |  
|Total operating expenses                                      |  |                              | 20,353,601  |   |      |   | 16,969,602  |  
|                                                              |  |                              |             |   |      |   |             |  
|Loss from operations                                          |  |                              | (13,673,941 | ) |      |   | (10,758,578 | )
|Interest income, net                                          |  |                              | 486,601     |   |      |   | 1,703,019   |  
|                                                              |  |                              |             |   |      |   |             |  
|Net loss                                                      |  | $                            | (13,187,340 | ) |      | $ | (9,055,559  | )
|                                                              |  |                              |             |   |      |   |             |  
|Basic and diluted net loss per share                          |  | $                            | (0.28       | ) |      | $ | (0.20       | )
|                                                              |  |                              |             |   |      |   |             |  
|Shares used in computing basic and diluted net loss per share |  |                              | 46,296,235  |   |      |   | 45,948,066  |  
|                                                              |  |                              |             |   |      |   |             |  

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



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ADOLOR CORPORATION

Statement of Stockholders Equity

(Unaudited)



|                                                        |  |                 |  |                          |       |                                               |   |             |                    |   |          |                          |  |   |              |   |  |   |             |  
|------------------------------------------------------- |  | --------------- |  | ------------------------ | ----- | --------------------------------------------- | - | ----------- | ------------------ | - | -------- | ------------------------ |  | - | ------------ | - |  | - | ----------- | -
|                                                        |  | Common stock    |  | Additionalpaid-incapital |       | Unrealizedgainson availablefor salesecurities |   |             | Accumulateddeficit |   |          | Totalstockholdersequity | 
|                                                        |  | Numberof shares |  | Amount                   |       |                                               |   |            
|Balance, January 1, 2009                                |  | 46,333,735      |  | $                        | 4,633 |                                               | $ | 543,009,215 |                    | $ | 671,457  |                          |  | $ | (455,066,743 | ) |  | $ | 88,618,562  |  
|Compensation expense under SFAS 123R                    |  |                |  |                          |      |                                               |   | 1,133,771   |                    |   |         |                          |  |   |             |   |  |   | 1,133,771   |  
|Unrealized losses on available for sale securities, net |  |                |  |                          |      |                                               |   |            |                    |   | (413,384 | )                        |  |   |             |   |  |   | (413,384    | )
|Net loss                                                |  |                |  |                          |      |                                               |   |            |                    |   |         |                          |  |   | (13,187,340  | ) |  |   | (13,187,340 | )
|                                                        |  |                 |  |                          |       |                                               |   |             |                    |   |          |                          |  |   |              |   |  |   |             |  
|Balance, March 31, 2009                                 |  | 46,333,735      |  | $                        | 4,633 |                                               | $ | 544,142,986 |                    | $ | 258,073  |                          |  | $ | (468,254,083 | ) |  | $ | 76,151,609  |  
|                                                        |  |                 |  |                          |       |                                               |   |             |                    |   |          |                          |  |   |              |   |  |   |             |  

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



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ADOLOR CORPORATION

Statements of Cash Flows

(Unaudited)



|                                                                            |  |                              |             |   |      |   |             |  
|--------------------------------------------------------------------------- |  | ---------------------------- | ----------- | - | ---- | - | ----------- | -
|                                                                            |  | Three Months Ended March 31, |            
|                                                                            |  | 2009                         |             |   | 2008 |  
|Net cash flows from operating activities:                                   |  |                              |             |   |      |   |             |  
|Net loss                                                                    |  | $                            | (13,187,340 | ) |      | $ | (9,055,559  | )
|Adjustments to reconcile net loss to net cash used in operating activities: |  |                              |             |   |      |   |             |  
|Stock-based compensation expense                                            |  |                              | 1,133,371   |   |      |   | 1,547,863   |  
|Amortization of premiums and discounts on short-term investments            |  |                              | 393,229     |   |      |   | 142,797     |  
|Amortization of deferred revenue and rent                                   |  |                              | (3,458,318  | ) |      |   | (4,403,248  | )
|Depreciation and amortization expense                                       |  |                              | 527,493     |   |      |   | 569,554     |  
|Changes in assets and liabilities:                                          |  |                              |             |   |      |   |             |  
|Accounts receivable                                                         |  |                              | 2,229,384   |   |      |   | (256,398    | )
|Inventory                                                                   |  |                              | (144,390    | ) |      |   |            |  
|Prepaid expenses and other current assets                                   |  |                              | 177,381     |   |      |   | 27,174      |  
|Other assets                                                                |  |                              | (6,999      | ) |      |   | 13,775      |  
|Accounts payable                                                            |  |                              | (62,148     | ) |      |   | 318,413     |  
|Accrued expenses                                                            |  |                              | (2,550,526  | ) |      |   | (722,934    | )
|Customer deposits                                                           |  |                              | 377,415     |   |      |   |            |  
|Deferred revenue                                                            |  |                              | 8,425,000   |   |      |   |            |  
|                                                                            |  |                              |             |   |      |   |             |  
|Net cash used in operating activities                                       |  |                              | (6,146,448  | ) |      |   | (11,818,563 | )
|                                                                            |  |                              |             |   |      |   |             |  
|Net cash flows from investing activities:                                   |  |                              |             |   |      |   |             |  
|Purchases of equipment and leasehold improvements, net of disposals         |  |                              | (285,016    | ) |      |   | (454,100    | )
|Purchases of short-term investments                                         |  |                              | (19,948,064 | ) |      |   | (46,754,500 | )
|Maturities of short-term investments                                        |  |                              | 36,000,000  |   |      |   | 55,500,000  |  
|                                                                            |  |                              |             |   |      |   |             |  
|Net cash provided by investing activities                                   |  |                              | 15,766,920  |   |      |   | 8,291,400   |  
|                                                                            |  |                              |             |   |      |   |             |  
|Net cash flows from financing activities:                                   |  |                              |             |   |      |   |             |  
|Net proceeds from exercise of stock options                                 |  |                              |            |   |      |   | 3,510       |  
|                                                                            |  |                              |             |   |      |   |             |  
|Net cash provided by financing activities                                   |  |                              |            |   |      |   | 3,510       |  
|                                                                            |  |                              |             |   |      |   |             |  
|Net increase (decrease) in cash and cash equivalents                        |  |                              | 9,620,472   |   |      |   | (3,523,653  | )
|Cash and cash equivalents at beginning of period                            |  |                              | 7,535,146   |   |      |   | 15,575,804  |  
|                                                                            |  |                              |             |   |      |   |             |  
|Cash and cash equivalents at end of period                                  |  | $                            | 17,155,618  |   |      | $ | 12,052,151  |  
|                                                                            |  |                              |             |   |      |   |             |  
|Supplemental disclosure of cash flow information:                           |  |                              |             |   |      |   |             |  
|Unrealized gains (losses) on available for sale securities, net             |  | $                            | (413,384    | ) |      | $ | 437,082     |  
|Change in accrued expenses related to purchases of equipment                |  |                              | 20,712      |   |      |   | (387,240    | )

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



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Adolor Corporation

Notes to Financial Statements

March 31, 2009

(Unaudited)



|1. | ORGANIZATION AND BUSINESS ACTIVITIES
|-- | ------------------------------------

Adolor Corporation (the Company) is a biopharmaceutical company focused on the discovery,
development and commercialization of novel prescription pain management products. On May 20, 2008, the U.S. Food and Drug Administration (FDA) approved the Companys first product, ENTEREG® (alvimopan), for the management of postoperative ileus following bowel resection surgery (POI). POI causes significant discomfort for patients and results in increased expense to healthcare providers. ENTEREG is
specifically indicated to accelerate the time to upper and lower gastrointestinal recovery following partial large or small bowel resection surgery with primary anastomosis. In collaboration with Glaxo Group Limited (Glaxo), the Company launched
ENTEREG in the United States in mid-2008.

The Company also has a number of product candidates in various stages of clinical and
preclinical development. The Company is collaborating with Pfizer Inc. (Pfizer) in the clinical development of two delta opioid receptor agonist compounds, ADL5859 and ADL5747 (Pfizer compounds PF-04856880 and PF-04856881, respectively), for
the treatment of pain. The Company is developing ADL7445 to treat opioid bowel dysfunction, a condition that often results from chronic use of opioid analgesics to treat persistent pain conditions. ADL7445 is in preclinical development and the
Company intends to submit an Investigational New Drug Application in the third quarter of 2009. The Companys other product candidates are in preclinical development for treating moderate-to-severe pain and other central nervous system
conditions.

Interim Financial Information

The accompanying unaudited financial statements have been prepared in accordance with U.S. generally accepted accounting principles for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X.
Accordingly, they do not include all of the information and footnote disclosures required by U.S. generally accepted accounting principles for complete financial statements. In the opinion of management, all adjustments (consisting only of normal
recurring adjustments) considered necessary for a fair presentation have been included. These financial statements should be read in conjunction with the financial statements and notes thereto included in the Companys Annual Report on
Form 10-K, filed with the Securities and Exchange Commission (SEC), which includes audited financial statements at December 31, 2008 and 2007 and for each of the years in the three-year period ended December 31, 2008. The results of
the Companys operations for any interim period are not necessarily indicative of the results of operations for any other interim period or full year.

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the
United States requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenues and expenses and related disclosure of assets and liabilities. The estimates made are principally in the areas of
revenue recognition, research and development accruals and stock-based compensation expense. Management bases its estimates on historical experience and various assumptions that are believed to be reasonable under the circumstances. Actual results
may differ from those estimates.

Product Sales Recognition

In accordance with SEC Staff Accounting Bulletin (SAB) No. 101, Revenue Recognition in Financial Statements, as amended by SAB No. 104, Revenue Recognition, and Statement of Financial
Accounting Standards (SFAS) No. 48, Revenue Recognition When Right of Return Exists, the Company defers recognition of revenue associated with the first shipment of ENTEREG to each hospital customer as it is not yet able to reasonably
estimate future returns. When an existing customer places a new order, the Company recognizes revenue on the previous shipment for an amount equal to the lesser of (a) the previous shipment or (b) the new order. Hospital orders are
processed through wholesalers; however, ENTEREG is drop-shipped from Glaxos warehouse directly to an ordering hospital registered under the ENTEREG Access Support and Education (E.A.S.E.) Program. Once the Company has developed
sufficient historical experience to estimate product returns, it intends to recognize net product sales upon the transfer of ownership and risk of loss for the product to the customer.



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The Company records product sales net of prompt payment discounts, returns and other discounts as
reported to it by Glaxo. When payment from Glaxo is received but the conditions for revenue recognition have not yet been met, the Company will record a liability, which is classified on the balance sheet as customer deposits.

Adjustment to Statement of Cash Flows

Management has
determined that the amortization of premiums and discounts on short-term investments previously included within net cash provided by investing activities in the first quarter of 2008 should have been included as a non-cash adjustment in net cash
used in operating activities in the Companys statement of cash flows. This adjustment resulted in an approximately $0.1 million decrease in net cash used in operating activities and in net cash provided by investing activities for the quarter
ended March 31, 2008 and had no impact on any amounts on the balance sheet, statement of operations or on the net decrease in cash and cash equivalents reflected in the statement of cash flows. Management believes that the impact of this
adjustment is not material to the Companys financial position, results of operations or liquidity for the quarter ended March 31, 2008.



|2. | RECENT ACCOUNTING PRONOUNCEMENTS
|-- | --------------------------------

In December 2007,
the Financial Accounting Standards Board issued Emerging Issues Task Force (EITF) Issue No. 07-1, Accounting for Collaborative Arrangements, which applies to collaborative arrangements that are conducted by the participants without the
creation of a separate legal entity for the arrangement and clarifies, among other things, how to determine whether a collaborative arrangement is within the scope of this issue. EITF Issue No. 07-1 is effective for financial statements issued
for fiscal years beginning after December 15, 2008. The adoption of EITF Issue No. 07-1 did not impact the Companys results of operations or financial position.



|3. | COMPREHENSIVE LOSS
|-- | ------------------

The following is the
reconciliation of net loss to comprehensive loss for the three months ended March 31, 2009 and 2008:



|                                                                |  |                              |             |   |      |   |            |  
|--------------------------------------------------------------- |  | ---------------------------- | ----------- | - | ---- | - | ---------- | -
|                                                                |  | Three Months Ended March 31, |            
|                                                                |  | 2009                         |             |   | 2008 |  
|Net loss                                                        |  | $                            | (13,187,340 | ) |      | $ | (9,055,559 | )
|Unrealized gains (losses) on available for sale securities, net |  |                              | (413,384    | ) |      |   | 437,082    |  
|                                                                |  |                              |             |   |      |   |            |  
|Comprehensive loss                                              |  | $                            | (13,600,724 | ) |      | $ | (8,618,477 | )
|                                                                |  |                              |             |   |      |   |            |  



|4. | SHORT-TERM INVESTMENTS
|-- | ----------------------

Short-term investments
consist of U.S. Treasury obligations with original maturities of greater than three months. All investments are classified as available for sale and are considered current assets as the contractual maturities of the Companys short-term
investments are all less than one year.

The following summarizes the short-term investments at March 31, 2009 and December 31,
2008:



|                                                 |  |      |             |                      |   |                       |  |   |            |   |  |   |            
|------------------------------------------------ |  | ---- | ----------- | -------------------- | - | --------------------- |  | - | ---------- | - |  | - | -----------
|                                                 |  | Cost |             | GrossUnrealizedGains |   | GrossUnrealizedLosses |  |   | Fair Value
|U.S. Government obligations at March 31, 2009    |  | $    | 107,258,438 |                      | $ | 265,138               |  | $ | (7,065     | ) |  | $ | 107,516,511
|                                                 |  |      |             |                      |   |                       |  |   |            |   |  |   |            
|U.S. Government obligations at December 31, 2008 |  | $    | 123,703,603 |                      | $ | 671,457               |  | $ |           |   |  | $ | 124,375,060
|                                                 |  |      |             |                      |   |                       |  |   |            |   |  |   |            

Statement of Financial Accounting Standards (SFAS) No. 157, Fair Value
Measurements, establishes a valuation hierarchy for disclosure of the inputs to valuation techniques used to measure fair value. This hierarchy prioritizes the inputs into three broad levels. Level 1 inputs are quoted prices (unadjusted) in
active markets for identical assets or liabilities. Level 2 inputs include quoted prices for identical or similar assets and liabilities in



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markets that are not active, quoted prices for similar assets and liabilities in active markets or inputs that are observable for the asset or liability,
either directly or indirectly through market corroboration, for substantially the full term of the financial instrument. Level 3 inputs are unobservable inputs based on managements own assumptions used to measure assets and liabilities at fair
value. The classification of a financial asset or liability within the hierarchy is determined based on the lowest level input that is significant to the fair value measurement.

The following table provides the Companys assets and liabilities carried at fair value as of March 31, 2009:



|                       |  |                                        |             |                                                 |   |                                           |  |                                        |   |  |   |  
|---------------------- |  | -------------------------------------- | ----------- | ----------------------------------------------- | - | ----------------------------------------- |  | -------------------------------------- | - |  | - | -
|                       |  |                                        |             | Fair Value Measurements at March 31, 2009 using
|                       |  | Total CarryingValue as ofMarch 31,2009 |             | Quoted PricesinActive Markets(Level 1)          |   | SignificantOtherObservableInputs(Level
2) |  | SignificantUnobservableInputs(Level 3)
|Short-term investments |  | $                                      | 107,516,511 |                                                 | $ | 107,516,511                               |  | $                                      |  |  | $ | 
|                       |  |                                        |             |                                                 |   |                                           |  |                                        |   |  |   |  



|5. | INVENTORY
|-- | ---------

At March 31, 2009, inventory
consists of $0.1 million of work in progress performed subsequent to the approval of ENTEREG by the FDA. Inventories are stated at the lower of cost or market, as determined on a first-in, first-out, or FIFO, basis. All other inventory purchases for
unapproved product candidates, including ENTEREG inventory costs incurred prior to FDA approval, are recorded as research and development expense when incurred. The Company periodically reviews its inventory for excess or obsolete inventory, and
will write-down the excess or obsolete inventory value to its net realizable value, if applicable.



|6. | CONTRACT REVENUES
|-- | -----------------

Contract revenues for the three
months ended March 31, 2009 and 2008 consist of the following:



|                                                  |  |                             |           |      |   |          
|------------------------------------------------- |  | --------------------------- | --------- | ---- | - | ---------
|                                                  |  | Three Months EndedMarch 31,
|                                                  |  | 2009                        |           | 2008
|Amortization of deferred revenue                  |  | $                           | 3,415,386 |      | $ | 4,362,617
|Cost reimbursement under collaboration agreements |  |                             | 1,832,091 |      |   | 1,848,407
|                                                  |  |                             |           |      |   |          
|                                                  |  |                            
|Total contract revenues                           |  | $                           | 5,247,477 |      | $ | 6,211,024
|                                                  |  |                             |           |      |   |          

In April 2002, the Company entered into a collaboration agreement with Glaxo for the exclusive
worldwide development and commercialization of ENTEREG for certain indications. Under the terms of the agreement, Glaxo paid the Company a non-refundable and non-creditable signing fee of $50.0 million. The $50.0 million signing fee was recorded as
deferred revenue and is being recognized as revenue on a straight-line basis over the estimated performance period under the collaboration agreement, which extends to March 2016. Revenue related thereto of $0.8 million was recognized in each of the
three-month periods ended March 31, 2009 and 2008.

External expenses for research and development and marketing activities incurred
in the United States by each party are reimbursed pursuant to contractually agreed percentages. Reimbursement amounts owed to the Company by Glaxo are recorded gross in the statements of operations as contract revenues. The Company recorded
collaboration agreement cost reimbursements from Glaxo of $1.3 million and $1.0 million in the three months ended March 31, 2009 and 2008, respectively, under this arrangement. As of March 31, 2009, $0.8 million was receivable from Glaxo
for reimbursement of expenses incurred by the Company pursuant to the collaboration agreement.

In January 2009, the Company and Glaxo
entered into Amendment No. 4 to the collaboration agreement. Under Amendment No. 4, the Company and Glaxo, effective as of January 1, 2009, modified certain provisions of the collaboration agreement (i) to reflect the current
plan jointly developed by the parties relating to the sale and promotion of ENTEREG and (ii) to modify certain payment provisions of the collaboration



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agreement, principally the acceleration of payments owed by Glaxo to the Company. Under the terms of Amendment No. 4, Glaxo paid the Company $8.4
million during the three months ended March 31, 2009. In accordance with EITF Issue No. 00-21, Revenue Arrangements with Multiple Deliverables, the Company determined that the payment should be evaluated as part of a single arrangement
with multiple deliverables under the collaboration agreement. Further, the Company determined that the payment did not meet the criteria of EITF Issue No. 00-21 to be accounted for as a separate unit of accounting under the arrangement and, as a
result, the $8.4 million was recorded as deferred revenue and is being recognized as revenue on a straight-line basis over the estimated remaining performance period under the collaboration agreement. Revenue related thereto of $0.1 million was
recognized in the three months ended March 31, 2009. Under the terms of Amendment No. 4, the Company also will receive a payment from Glaxo in the second quarter of 2009 that is expected to total approximately $0.9 million.

In December 2007, the Company entered into a collaboration agreement with Pfizer for the exclusive worldwide development and commercialization of ADL5859
and ADL5747. Under the terms of the agreement, Pfizer paid the Company an up-front payment of $30.0 million and reimbursed $1.9 million of Phase 2a development costs incurred by the Company prior to entering into the collaboration agreement. The
$31.9 million up-front fee was recorded as deferred licensing fees and is being recognized as revenue on a straight-line basis over the estimated performance period under the collaboration agreement. During the third quarter of 2008, the performance
period was extended by six months to August 2010 based on the status of the development programs. During the first quarter of 2009, the performance period was further extended by four months to December 2010 based on the current status of the
development programs. The effect of this change in estimate was a reduction in contract revenues of $0.2 million for the three months ended March 31, 2009. The Company recorded amortization of deferred license fees under the collaboration
agreement with Pfizer of $2.5 million and $3.5 million in the three months ended March 31, 2009 and 2008, respectively.

External
expenses for research and development and marketing activities incurred in the United States by each party are reimbursed pursuant to contractually agreed percentages. Reimbursement amounts owed to the Company by Pfizer are recorded gross on the
statements of operations as contract revenues. The Company recorded collaboration cost reimbursement from Pfizer of $0.5 million and $0.8 million in the three months ended March 31, 2009 and 2008, respectively. As of March 31, 2009, $0.5
million was receivable from Pfizer for reimbursement of expenses incurred by the Company pursuant to the collaboration agreement.



|7. | STOCKHOLDERS EQUITY
|-- | --------------------

During the three months
ended March 31, 2009, the Company granted options to purchase 1,066,211 shares of common stock to employees and non-employee directors. The employee stock options vest monthly over a four-year period beginning from the date of grant; the
non-employee director stock options vest annually over a two-year period beginning from the date of grant. All stock options were granted with an exercise price equal to the fair market value of the Companys common stock on the date of grant.
The grant-date fair value of the options granted during the three months ended March 31, 2009 was $1.3 million, and such amounts will be recognized over the applicable vesting period.

During the three months ended March 31, 2009, the Company granted 303,043 deferred stock awards to employees. Of these awards, 130,000 shares were
granted to members of executive management and vest upon the achievement of certain sales targets within a specified period of time. In accordance with SFAS No. 123R, Share-Based Payment, the Company will begin recognizing compensation
cost for these performance shares if and when it is probable the performance condition will be achieved. The remaining 173,043 deferred stock awards vest annually over a four-year period beginning from the date of grant and will be expensed
over the applicable vesting period. The fair value of all deferred stock awards granted during the three months ended March 31, 2009 was $0.5 million.

For the three months ended March 31, 2009, compensation expense recognized related to outstanding stock options as well as deferred and restricted stock awards was $1.1 million.



|8. | LEGAL PROCEEDINGS
|-- | -----------------

On April 21, 2004, a
lawsuit was filed in the U.S. District Court for the Eastern District of Pennsylvania against the Company, one of its directors and certain of its officers seeking unspecified damages on behalf of a putative class of persons who purchased Adolor
common stock between September 23, 2003 and January 14, 2004. The complaint alleges violations of Section 10(b) and Section 20(a) of the Securities Exchange Act of 1934, in



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connection with the announcement of the results of certain studies in the Companys Phase 3 clinical trials for alvimopan, which allegedly had the
effect of artificially inflating the price of the Companys common stock. This suit has been consolidated with three subsequent actions asserting similar claims under the caption In re Adolor Corporation Securities Litigation,No. 2:04-cv-01728. On December 29, 2004, the District Court issued an order appointing the Greater Pennsylvania Carpenters Pension Fund as Lead Plaintiff. The appointed Lead Plaintiff filed a consolidated amended complaint on
February 28, 2005. That complaint purported to extend the class period, so as to bring claims on behalf of a putative class of Adolor shareholders who purchased stock between September 23, 2003 and December 22, 2004. The complaint
also adds as defendants the Companys Board of Directors asserting claims against them and the other defendants for violation of Section 11 and Section 15 of the Securities Act of 1933 in connection with the Companys public
offering of stock in November 2003. Together with the management and director defendants, the Company moved to dismiss the complaint on April 29, 2005. The plaintiffs responded to the motion to dismiss on June 28, 2005, and the
Companys reply was filed on August 12, 2005.

On August 2, 2004, two shareholder derivative lawsuits were filed in the U.S.
District Court for the Eastern District of Pennsylvania, purportedly on behalf of the Company, against its directors and certain of its officers seeking unspecified damages for various alleged breaches of fiduciary duty and waste. The allegations
are similar to those set forth in the class action complaints, involving the announcement of the results of certain studies in the Companys Phase 3 clinical trials for alvimopan. On November 12, 2004, the derivative plaintiff filed an
amended complaint. On December 13, 2004, the Company filed a motion challenging the standing of the derivative plaintiff to file the derivative litigation on its behalf. On December 13, 2004, the Companys directors and officers moved
to dismiss the complaint for the failure to state a claim. Plaintiffs responded to these motions on January 27, 2005 and the Company filed reply briefs on February 18, 2005.

The Company believes that the allegations in each of these matters are without merit and intends to vigorously defend against the litigation. The Company
has not accrued any amount in its financial statements as of March 31, 2009 for these matters, and the Company awaits the decision of the District Court in each matter.



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

Managements Discussion and Analysis of Financial Condition and Results of Operations (MD&A) is intended to provide information to assist you
in better understanding and evaluating our financial condition and results of operations. We encourage you to read this MD&A in conjunction with our financial statements, included in Part I, Item 1 of this Quarterly Report on Form 10-Q, and
our Annual Report on Form 10-K for the year ended December 31, 2008.

EXECUTIVE SUMMARY

We are a biopharmaceutical company focused on the discovery, development and commercialization of
novel prescription pain management products. On May 20, 2008, the U.S. Food and Drug Administration (FDA) approved our first product, ENTEREG® (alvimopan), for the management of
postoperative ileus following bowel resection surgery (POI). POI causes significant discomfort for patients and results in increased expense to healthcare providers. ENTEREG is specifically indicated to accelerate the time to upper and lower
gastrointestinal (GI) recovery following partial large or small bowel resection surgery with primary anastomosis. We also have a number of product candidates in various stages of clinical and preclinical development.

For the three months ended March 31, 2009, our total revenues and net loss were $6.7 million and $13.2 million, respectively. Net
shipments of ENTEREG for the three months ended March 31, 2009 were $2.0 million, of which we recognized $1.4 million as net product sales under our revenue recognition policy. We will need sales of ENTEREG to increase significantly beyond
current levels before we will be able to achieve profitability and positive cash flow from operations. Ultimately, we may never generate sufficient revenues from ENTEREG for us to reach profitability, generate positive cash flow or sustain, on an
ongoing basis, our current or projected levels of operations.

ENTEREG for POI

Together with our partner, Glaxo Group Limited (Glaxo), we launched ENTEREG in the United States in mid-2008. ENTEREG is detailed primarily by
Glaxos national hospital-based sales organization. We are co-promoting ENTEREG in certain hospitals with a field force that now numbers approximately 25 persons.ENTEREG was approved in POI subject to a Risk Evaluation and Mitigation
Strategy (REMS) under which the product is available only to hospitals that perform bowel resections and are enrolled in the ENTEREG Access Support and Education (E.A.S.E.) Program. As of March 31, 2009, approximately 1,275 hospitals have
registered under the E.A.S.E. program. Additionally, as of March 31, 2009, we estimate that approximately 425 hospitals had accepted ENTEREG for inclusion on their formularies, including 275 of the 1,400 hospitals that perform approximately 80%
of the bowel resection surgeries in the United States.

Under our agreement with Glaxo, we have a profit-sharing arrangement under which we
receive 45% and Glaxo receives 55% of profits, as defined. Profits are calculated as net sales of ENTEREG less certain agreed-upon costs and are subject to certain adjustments. Beginning in mid-2011, the parties will share such profits equally.

In 2009, there are a number of initiatives being addressed to potentially increase the awareness and acceptance of ENTEREG among hospitals
and physicians performing bowel resection surgeries. These efforts will include analysis intending to address pharmacoeconomic and health outcomes associated with accelerated GI recovery. Longer-term, Glaxo and we are evaluating additional clinical
studies of ENTEREG for POI resulting from pain management following surgical procedures other than bowel resection surgeries. As required by our FDA approval letter for ENTEREG, we recently began a Phase 4 clinical trial intended to evaluate the
safety and efficacy of ENTEREG for POI in patients undergoing radical cystectomy for bladder cancer.

DeltaOpioid Receptor
Agonists

We are collaborating with Pfizer Inc. (Pfizer) for the development and commercialization of thedelta opioid receptor
agonist compounds, ADL5859 and ADL5747 (Pfizer compounds PF-04856880 and PF-04856881), for the treatment of pain. Thedelta receptor is one of three opioid receptors that modulate pain. Today, all marketed opioid drugs interact primarily with
themu receptor. We have identified a series of novel, orally-activedelta agonists that selectively stimulate thedelta opioid receptor. Our goal is to develop medications that produce pain relief similar to traditionalmuopioids, while reducing or eliminating some typical narcotic side effects.



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We have completed three Phase 2a studies of the initial formulation of ADL5859 in (i) acute pain
after surgical removal of impacted third molars, (ii) pain associated with rheumatoid arthritis and (iii) pain associated with diabetic peripheral neuropathy. While ADL5859 was well tolerated in these studies, ADL5859 showed no
statistically significant difference versus placebo in these trials. Pfizer and we have re-formulated ADL5859 to address the pharmacokinetic variability observed in these Phase 2a trials and have initiated certain pharmacokinetic studies of ADL5859
as well as ADL5747. Pfizer and we intend to initiate proof-of-concept trials of re-formulated ADL5859 and ADL5747 later in 2009.

Opioid Bowel
Dysfunction Program

Opioid receptors in the GI tract, or peripheral opioid receptors, regulate functions such as motility and water
secretion and absorption. Stimulation of these GI mu-opioid receptors by morphine, or other opioid analgesics, can slow gut motility and disrupt normal GI function that allows for the passage, absorption and excretion of ingested solid
materials resulting in a number of symptoms, including severe constipation. In patients who take opioid analgesics to treat chronic and persistent pain, this condition is known as opioid bowel dysfunction (OBD).

We are developing ADL7445 to treat OBD. ADL7445 is a proprietary, small molecule, peripherally-acting mu-opioid receptor antagonist intended to
block the adverse effects of opioid analgesics on the GI tract without affecting analgesia. ADL7445 has demonstrated safety and efficacy in preclinical models and we are targeting the third quarter of 2009 for the submission of an Investigational
New Drug Application (IND).

Discovery Research and In-licensing Efforts

Our pain research efforts initially focused on designing small molecules to target opioid receptors as a means of improving the benefit-to-risk profile of
currently available opioid analgesics. While work continues on the selective targeting of opioid receptors, we also are seeking to use advancements in molecular biology and medicinal chemistry to design molecules that target other, non-opioid, pain
receptors and other central nervous system targets. Through our internal discovery effort, we have several product candidates in preclinical development intended to address the treatment of moderate-to-severe pain.

We believe there may be opportunities to expand our product portfolio through the acquisition or in-licensing of products and/or product development
candidates and intend to continue to explore and evaluate such opportunities.

LIQUIDITY AND CAPITAL RESOURCES

Cash, cash equivalents and short-term investments were $124.7 million at March 31, 2009 and $131.9 million at December 31, 2008, representing
93% and 91% of our total assets, respectively. We invest excess cash in U.S. Treasury obligations. Our working capital, which is calculated as current assets less current liabilities, was $105.7 million at March 31, 2009 compared to $112.3
million at December 31, 2008. The decrease in cash, cash equivalents and short-term investments and working capital was primarily from the use of cash to fund our operations, offset partially by $8.4 million received from Glaxo as a result of
the modification of certain payment provisions under our collaboration agreement.

The following is a summary of selected cash flow
information for the three months ended March 31, 2009 and 2008:



|                                          |  |                              |             |   |      |   |             |  
|----------------------------------------- |  | ---------------------------- | ----------- | - | ---- | - | ----------- | -
|                                          |  | Three Months Ended March 31, |            
|                                          |  | 2009                         |             |   | 2008 |  
|Net loss                                  |  | $                            | (13,187,340 | ) |      | $ | (9,055,559  | )
|Adjustments for non-cash operating items  |  |                              | (1,404,225  | ) |      |   | (2,143,034  | )
|                                          |  |                              |             |   |      |   |             |  
|Net cash operating loss                   |  |                              | (14,591,565 | ) |      |   | (11,198,593 | )
|Net change in assets and liabilities      |  |                              | 8,445,117   |   |      |   | (619,970    | )
|                                          |  |                              |             |   |      |   |             |  
|Net cash used in operating activities     |  | $                            | (6,146,448  | ) |      | $ | (11,818,563 | )
|                                          |  |                              |             |   |      |   |             |  
|Net cash provided by investing activities |  | $                            | 15,766,920  |   |      | $ | 8,291,400   |  
|                                          |  |                              |             |   |      |   |             |  
|Net cash provided by financing activities |  | $                            |            |   |      | $ | 3,510       |  
|                                          |  |                              |             |   |      |   |             |  



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Net Cash Used in Operating Activities

Net cash used in operating activities of $6.1 million and $11.8 million for the three months ended March 31, 2009 and 2008, respectively, resulted
primarily from research and development expenditures associated with our product candidates and selling, general and administrative expenses, offset by payments received under the Glaxo and Pfizer collaboration agreements. For the three months ended
March 31, 2009 and 2008, we received net payments of $10.8 million and $1.6 million, respectively, under such collaboration agreements. Of the $10.8 million received during the three months ended March 31, 2009, $8.4 million was related to
the acceleration of payments owed by Glaxo to the Company under the terms of Amendment No. 4 of the Glaxo collaboration agreement. In addition, we received $1.8 million of cash related to net shipments of ENTEREG during the three months ended
March 31, 2009.

Net Cash Provided By Investing Activities

Net cash provided by investing activities relates to purchases and maturities of investment securities, as well as capital expenditures for property and equipment. We expect to fund a significant portion of our future
operations through the sale or maturities of investments in our portfolio, which consist of U.S. Treasury obligations.

Net cash provided
by investing activities was $15.8 million for the three months ended March 31, 2009 as compared to $8.3 million for the three months ended March 31, 2008. The increase in cash provided by investing activities for the three months
ended March 31, 2009 is primarily attributable to an increase in cash provided from the net maturities of available-for-sale securities.

Outlook

We expect to use our cash, cash equivalents and short-term investments for working capital and to fund our operations. Since inception,
we have experienced significant operating losses and negative operating cash flow and have funded our operations primarily from the proceeds received from the sale of our equity securities, as well as from amounts received under collaboration
agreements. Our accumulated deficit at March 31, 2009 was $468.3 million and we expect to continue to incur substantial losses for at least the next several years.

We may never generate significant product sales, achieve profitable operations or generate positive cash flows from operations and, even if profitable operations are achieved, they may not be sustained on a continuing
basis or sufficient to support our current or projected levels of investment in our research and development programs and our other operations. At this time, we cannot accurately assess a number of factors that will influence the levels of future
product sales, such as the degree of market acceptance, patent protection and exclusivity of ENTEREG, the impact of competition, the effectiveness of our sales and marketing efforts and the outcome of our current efforts to develop, receive approval
for and successfully launch other product candidates. However, we will need sales of ENTEREG to increase significantly beyond current levels before we will be able to achieve profitability and positive cash flows from operations. We believe that our
existing cash, cash equivalents and short-term investments are adequate to fund our operations into 2011 based upon the level of research and development and marketing and administrative activities we believe will be necessary to achieve our
strategic objectives. We may need to obtain funding for our future operational needs, and we cannot be certain that funding will be available on terms acceptable to us, or at all.

ENTEREG

Our ability to generate
positive cash flow from operations depends, in large part, on our ability to successfully commercialize ENTEREG in the United States. To that end, we expect that sales and marketing expenses associated with the product will continue to increase
during 2009. Prior to the FDA approval of ENTEREG, costs associated with the manufacture of alvimopan were expensed to research and development. As a result, at March 31, 2009, we have inventory related to alvimopan that carries a zero-cost and
is not reflected on the March 31, 2009 balance sheet. Certain of this inventory is expected to be used in further research and development activities, with the remaining inventory available for commercial sale. To the extent that this inventory
is sold, our cost of product sales will not reflect costs associated with such product manufacture, and our gross margins will be favorably impacted. We currently are unable to estimate the timing of the impact to future profitability resulting from
the sell-through of any inventory manufactured after FDA approval of ENTEREG for POI.



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Research and Development

Over the past few years, we have incurred significant expenditures related to conducting clinical studies to develop new pharmaceutical products. We
expect to continue to incur significant levels of research and development expenditures related to our preclinical and clinical product candidates. We expect to begin or continue a number of clinical programs including, among others, a Phase 4 study
of ENTEREG for the management of POI in patients undergoing radical cystectomy, additional Phase 1 and Phase 2a clinical trials of ADL5747 and ADL5859 and Phase 1 clinical trials for ADL7445. We also expect to continue to conduct research,
preclinical studies and process development activities on other product candidates. It is likely that expenses related to these efforts will increase over time should these programs advance to later stages of development.

RESULTS OF OPERATIONS

This section should be read
in conjunction with the discussion above under Liquidity and Capital Resources.

Product Sales

Net product sales are derived solely from ENTEREG. ENTEREG was approved by the FDA in May 2008 and product shipments to hospitals began in June 2008. In
accordance with SEC Staff Accounting Bulletin (SAB) No. 101, Revenue Recognition in Financial Statements, as amended by SAB No. 104, Revenue Recognition, and Statement of Financial Accounting Standards No. 48, Revenue
Recognition When Right of Return Exists, we defer recognition of revenue associated with the first shipment of ENTEREG to each hospital customer as we are not yet able to reasonably estimate future returns. When an existing customer places a new
order, we recognize product sales on the previous shipment for an amount equal to the lesser of (a) the previous shipment or (b) the new order. Hospital orders are processed through wholesalers; however, ENTEREG is drop-shipped from
Glaxos warehouse directly to a registered hospital. Wholesalers remit payment to Glaxo and, on a monthly basis, Glaxo remits the net proceeds to us. We record product sales net of prompt payment discounts, returns and other discounts as
reported to us by Glaxo. While we undertake certain procedures to review the reasonableness of this information, we cannot obtain absolute assurance over the accounting methods and controls over such information utilized by Glaxo.

Net shipments of ENTEREG for the three months ended March 31, 2009 were $2.0 million and we recognized net product sales of $1.4 million under our
revenue recognition policy during the three months ended March 31, 2009. Since our commercial launch in June 2008, approximately 300 hospitals have reordered ENTEREG. We have a customer deposit balance of $0.7 million at March 31, 2009.
Customer deposits represent net shipments made for which payment has been received from Glaxo, but which have not yet been recognized as product sales revenue.

No product sales were recognized prior to the third quarter of 2008.

Contract Revenues

Contract revenues are derived from our collaboration agreements with Glaxo and Pfizer and include milestone payments, cost reimbursement and amortization
of up-front license fees and other deferred revenue. Contract revenues were $5.2 million and $6.2 million in the three months ended March 31, 2009 and 2008, respectively. The decrease in 2009 compared to 2008 was driven by decreased Pfizer
contract revenues of $1.3 million due primarily to decreased amortization of deferred licensing fees resulting from increases to the estimated performance period during the third quarter of 2008 and the first quarter of 2009. This decrease was
partially offset by higher Glaxo contract revenues resulting from reimbursement under the ENTEREG profit-sharing arrangement and $0.1 million of revenue related to the amortization of the $8.4 million payment received from Glaxo during the three
months ended March 31, 2009 under the terms of Amendment No. 4 to the collaboration agreement. The $8.4 million payment is being recognized as revenue on a straight-line basis over the estimated remaining performance period under the
collaboration agreement, which extends to March 2016. See Note 6 to the financial statements in Part 1, Item 1 of this report.

Cost of Product
Sales

Cost of product sales was $0.2 million in the three months ended March 31, 2009 and consisted primarily of royalty payments
under certain alvimopan license agreements and FDA fees. Prior to the FDA approval of ENTEREG, costs associated with the manufacture of alvimopan were expensed to research and development. Since product shipped during the three months ended
March 31, 2009 was manufactured prior to FDA approval, no manufacturing costs were incurred or recorded in cost of product sales during the three months ended March 31, 2009.



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Research and Development Expenses

Our research and development expenses can be identified as internal or external expenses. External expenses include expenses incurred with clinical research organizations, contract manufacturers and other third-party
vendors. Internal expenses include expenses such as personnel, laboratory and overhead expenses.

Research and development expenses were
$12.3 million and $11.4 million for the three months ended March 31, 2009 and 2008, respectively, and consist of the following:



|                                                 |  |                              |            |      |   |           
|------------------------------------------------ |  | ---------------------------- | ---------- | ---- | - | ----------
|                                                 |  | Three Months Ended March 31,
|                                                 |  | 2009                         |            | 2008
|External research and development expenses:      |  |                              |            |      |   |           
|ENTEREG POI program                              |  | $                            | 1,120,339  |      | $ | 1,708,744 
|Delta agonist program                            |  |                              | 865,932    |      |   | 1,373,445 
|OBD program                                      |  |                              | 1,502,169  |      |   |          
|Other programs                                   |  |                              | 1,523,074  |      |   | 2,341,975 
|                                                 |  |                              |            |      |   |           
|Total external research and development expenses |  |                              | 5,011,514  |      |   | 5,424,164 
|Total internal research and development expenses |  |                              | 7,311,109  |      |   | 5,996,908 
|                                                 |  |                              |            |      |   |           
|Total research and development expenses          |  | $                            | 12,322,623 |      | $ | 11,421,072
|                                                 |  |                              |            |      |   |           

We report all expenses gross within our statements of operations in accordance with Emerging
Issues Task Force Issue No. 99-19, Reporting Revenue Gross as a Principal Versus Net as an Agent, and, as such, the above table does not reflect any cost reimbursements from our collaboration partners.

Total research and development expenses increased for the three months ended March 31, 2009 as compared to the three months ended March 31,
2008 primarily due to expenses related to the development of our OBD program and increased personnel costs. These increases were partially offset by lower costs of clinical studies incurred during 2009 in our delta agonist program, decreased
activity in our preclinical programs and lower expenses in our ENTEREG POI program.

There are significant risks and uncertainties inherent
in the preclinical and clinical studies associated with each of our research and development programs. These studies may yield varying results that could delay, limit or prevent the advancement of a program through the various stages of product
development and significantly impact the costs to be incurred, and time involved, in bringing a program to completion. As a result, the cost to complete such programs, as well as the period in which net cash inflows from significant programs are
expected to commence, are not reasonably estimable.

Selling, General and Administrative Expenses

Our selling, general and administrative expenses were $7.9 million and $5.5 million for the three months ended March 31, 2009 and 2008, respectively.
The increase in 2009 compared to 2008 was primarily driven by higher sales and marketing expenses associated with the commercialization of ENTEREG.

Interest Income, Net

Our interest income, net was $0.5 million and $1.7 million for the three months ended March 31,
2009 and 2008, respectively. This decrease was due to lower investment balances resulting primarily from the use of cash in operating activities and an overall decline in interest rates.

CRITICAL ACCOUNTING POLICIES AND ESTIMATES

Managements Discussion and Analysis of Financial
Condition and Results of Operations discusses our financial statements, which we have prepared in accordance with U.S. generally accepted accounting principles. In preparing these financial statements, we must make estimates and assumptions that
affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements and the



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reported amounts of revenues and expenses during the reporting period. We develop and periodically change these estimates and assumptions based on historical
experience and various other factors that we believe are reasonable under the circumstances. Actual results may differ from these estimates under different assumptions or conditions. A summary of significant accounting policies and a description of
accounting policies that are considered critical may be found in our Annual Report on Form 10-K for the year ended December 31, 2008 in the Critical Accounting Policies and Estimates section and the Recently Issued Accounting
Pronouncements section of Part II, Item 7 and in Note 2 to the financial statements within Part II, Item 8.



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

Our investment assets consist primarily of U.S. Treasury obligations. The market value of such investments fluctuates with current market interest rates. In general, as rates increase, the market value of a debt instrument would be expected
to decrease. The opposite also is true. To minimize such market risk, we have in the past held, and to the extent possible will continue in the future to hold, such debt instruments to maturity at which time the debt instrument will be redeemed at
its stated, or face, value. Due to the short duration and nature of these instruments, we do not believe that we have a material exposure to interest rate risk related to our investment portfolio. The investment portfolio at March 31, 2009
totaled $107.5 million, and the weighted-average yield-to-maturity was approximately 1.5% with maturities ranging up to 12 months.



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



|(a) | Evaluation of Disclosure Controls and Procedures
|--- | ------------------------------------------------

For the quarterly period ended March 31, 2009, we carried out an evaluation, under the supervision and with the participation of our management, including our President and Chief Executive Officer and our Senior Vice President, Finance
and Chief Financial Officer (the principal financial and accounting officer), of the effectiveness of the design and operation of our disclosure controls and procedures pursuant to Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of
1934, as amended, as of the end of the period covered by this report.

Our management, including our President and Chief Executive Officer
and our Senior Vice President, Finance and Chief Financial Officer, does not expect that our disclosure controls and procedures will prevent all errors or fraud. A control system, no matter how well designed and operated, can provide only
reasonable, not absolute, assurance that the objectives of the control system are met and our disclosure controls and procedures are designed to provide this reasonable assurance. Based upon the evaluation discussed above, our President and Chief
Executive Officer and our Senior Vice President, Finance and Chief Financial Officer concluded that, as of March 31, 2009, our disclosure controls and procedures were effective at providing such reasonable assurance.



|(b) | Changes in Internal Control over Financial Reporting
|--- | ----------------------------------------------------

There were no changes in our internal control over financial reporting during the three-month period ended March 31, 2009 that have materially affected, or are reasonably likely to materially affect, our internal control over financial
reporting.



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PART II. OTHER INFORMATION



|ITEM 1. | LEGAL PROCEEDINGS
|------- | -----------------

The information required by this
Item is incorporated by reference to Note 8 of the financial statements included in Part I, Item 1 of this Report.



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

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

We are and will continue to be highly dependent on the commercial success of ENTEREG for POI, and we may be unable to attain profitability and positive cash flow from
operations based solely on product sales of ENTEREG.

In May 2008, the FDA approved ENTEREG for use in the treatment of POI. ENTEREG is
for hospital use only and is available only to hospitals that have been registered under our E.A.S.E. Program. The commercial success of ENTEREG will depend on several factors, including the following:



| |  |  | the acceptance of ENTEREG in the medical community, particularly with respect to whether physicians, patients and healthcare payors view ENTEREG as safe and
effective for its labeled indication, and whether it carries with it an acceptable benefit-to-risk profile;
| | - |  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | the number of hospitals that register for the E.A.S.E. Program;
| | - |  | ---------------------------------------------------------------



| |  |  | the ability to obtain formulary acceptance for ENTEREG at registered hospitals;
| | - |  | -------------------------------------------------------------------------------



| |  |  | the effectiveness of Glaxos and our sales and marketing efforts;
| | - |  | -----------------------------------------------------------------



| |  |  | the occurrence of any side effects, adverse reactions or misuse (or any unfavorable publicity relating thereto) stemming from the use of ENTEREG; and
| | - |  | -----------------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | the development of competing products or therapies for the treatment of POI.
| | - |  | ----------------------------------------------------------------------------

Ultimately, we may never generate sufficient revenues from ENTEREG for us to reach profitability, generate positive cash flow or sustain, on an ongoing basis, our current or projected levels of operations.

Restrictions on ENTEREG may have the effect of limiting the commercial prospects for the product.

In April 2007, Glaxo and we announced the results of Study 014, a Phase 3 long-term safety study of alvimopan in patients taking opioids for chronic
non-cancer pain and experiencing OBD. Results from Study 014 showed numerically more myocardial infarctions and other cardiovascular serious adverse events reported by patients treated long-term with alvimopan in this study compared to placebo. As a
result, ENTEREG was approved by the FDA subject to a REMS. The FDA has determined that a REMS is necessary to ensure that the benefits of ENTEREG in POI outweigh the risks. Our ENTEREG product labeling carries a boxed warning that ENTEREG is
available only for short-term (15 doses) use in hospitalized patients. The REMS and the boxed warning may make it more difficult to market and sell ENTEREG. We will not be able to market and sell ENTEREG to hospitals that do not register for the
E.A.S.E. Program. Hospitals may be unwilling or unable to comply with the requirements for registration in the E.A.S.E. Program. For example, hospitals may not have systems, order sets, protocols or other measures in place to limit the use of
ENTEREG to no more than 15 doses per patient and to ensure in-hospital use only. Hospitals also may not have controls in place to ensure that ENTEREG will neither be dispensed for outpatient use nor be transferred to unregistered hospitals. In such
cases, we will be unable to register these hospitals in the E.A.S.E. Program. Further, even if we are successful in registering hospitals, there can be no assurance that such hospitals will order ENTEREG in meaningful amounts, if at all.

Selling a pharmaceutical product in the hospital setting presents certain challenges. Each hospital environment is different, and each hospitals
or hospital groups prescribing is influenced by a list of accepted drugs called a formulary. Most hospitals have a committee, often called a pharmacy and therapeutics (P&T) committee,



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which meets periodically to determine which pharmaceutical products to add to the formulary. Many factors are assessed by such committees, including the cost
of the drug and its pharmacoeconomic profile. Once a pharmaceutical is on formulary, it is easier for a physician within a hospital or hospital group to prescribe the drug. Hospital formulary approval is critical to the commercial success of ENTEREG
and we cannot assure you that a sufficient number of hospitals will include ENTEREG on their formulary.

Our product sales revenues from ENTEREG and
related financial results will likely fluctuate and may fail to meet market expectations, which may adversely affect our stock price.

Forecasting revenue is difficult, especially when there is little commercial history, the product is the first product approved for a particular indication and when the level of market acceptance of the product is uncertain. For ENTEREG,
the registration process required under the E.A.S.E. Program, as well as the P&T committee and formulary approval process, is likely to slow uptake of the product. As a result of these factors, it is likely that we will experience significant
fluctuations in ENTEREG product sales from period to period and/or that product sales may not meet market expectations, which may adversely affect our stock price. Other factors that may cause our financial results to fluctuate include the
achievement and timing of research and development milestones and other collaboration revenues, the cost and timing of clinical trials, marketing and other expenses and manufacturing or supply disruption.

Ourdeltaopioid receptor agonist program may not lead to successful drug candidates.

To date, no selective delta opioid receptor agonist compounds have been successfully developed and approved by the FDA or any other regulatory
authority. We are developing our delta agonists, ADL5859 and ADL5747, in collaboration with Pfizer. These product candidates are in early stage clinical development. Drug development is a highly uncertain process; our delta agonist
product candidates may not be safe or effective and we may not be successful in our delta agonist development program. Development of delta agonists may not lead to commercially successful products. The original formulation of ADL5859
did not achieve a statistically significant difference versus placebo in three Phase 2a clinical trials in three different models of pain.

If we
continue to incur significant operating losses, we may be unable to continue our operations.

We have generated operating losses in
each year since we began operations in November 1994, and our accumulated deficit as of March 31, 2009 was $468.3 million. Our losses have resulted principally from costs incurred in research and development, including clinical trials, and from
selling, general and administrative expenses associated with our operations. We expect to continue to generate substantial losses for at least the next several years to fund our sales and marketing and research and development activities. We cannot
be sure that we will ever achieve significant product revenue from ENTEREG or any of our other product candidates sufficient for us to generate positive cash flows from operations. Sales of ENTEREG will need to increase significantly beyond current
levels before we will be able to achieve profitability and positive cash flows from operations. Even if we are able to achieve this, we may be unable to maintain profitability on a continuing basis or at a level sufficient to support our current or
projected levels of continuing investment. We may need to obtain funding for our future operational needs, and we cannot be certain that such funding will be available on terms acceptable to us, if at all, particularly in light of current economic
and capital market conditions. Any capital raising necessary to continue our operations may be through one or a combination of approaches, which could include public and/or private financing, sale and/or partnering of one or more of our development
programs or other strategic initiatives. Any public or private financings may involve issuances of debt or common stock or other classes of our equity, which could further dilute existing stockholders percentage ownership. If we are unable to
obtain funding to support operations, we will be forced to curtail our operations and we will be unable to develop products successfully.

Our stock
price has been highly volatile, and your investment in our stock could decline significantly in value.

The market price for our common
stock has been, and may continue to be in the future, highly volatile. For example, during the period January 1, 2006 through March 31, 2009, the price of our common stock reached a low of $1.27 per share on December 19, 2008 and a
high of $27.80 per share on March 1, 2006.

The market price for our common stock is highly dependent on the performance of ENTEREG in
the market and the success of our product development efforts. Negative announcements, including, among others:



| |  |  | disappointing sales of ENTEREG;
| | - |  | -------------------------------



| |  |  | disappointing developments concerning our collaborations;
| | - |  | ---------------------------------------------------------



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| |  |  | negative clinical trial results or adverse regulatory decisions for our product candidates;
| | - |  | -------------------------------------------------------------------------------------------



| |  |  | adverse period-to-period fluctuations in our sales or operating results or financial results that fall below the markets expectations; or
| | - |  | ------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | legal challenges, disputes and/or other adverse developments impacting our patents or other proprietary products,
| | - |  | -----------------------------------------------------------------------------------------------------------------

could trigger a significant decline in the price of our common stock. In addition, external events, such as news concerning economic or market conditions in the general
economy or within our industry, the activities of our competitors or our customers, changes in U.S. or foreign government regulations impacting our industry or the movement of capital into or out of our industry, also are likely to affect the price
of our common stock, regardless of our operating performance.

Our success is highly dependent on the efforts of our collaborators, the efforts of our
third-party contractors and on our ability to secure future partnerships.

Because we have limited resources, we have entered into a
number of agreements with other pharmaceutical companies. These agreements may call for our partner to control or play a significant role in, among other things:



| |  |  | the development of a product candidate, including, among other things, toxicology, formulation and clinical research efforts;
| | - |  | -----------------------------------------------------------------------------------------------------------------------------



| |  |  | the design and execution of clinical studies;
| | - |  | ---------------------------------------------



| |  |  | the process of obtaining regulatory approval to market the product; and
| | - |  | -----------------------------------------------------------------------



| |  |  | the manufacturing, marketing and selling of any approved product.
| | - |  | -----------------------------------------------------------------

In each of these areas, our partners may not support fully our research and commercial interests since our program may compete for time, attention and resources with the internal programs of our corporate
collaborators. As such, we cannot be sure that our corporate collaborators will share our perspectives on the relative importance of our program, that they will commit sufficient resources to our program to move it forward effectively or that the
program will advance as rapidly as it might if we had retained complete control of all research, development, regulatory and commercialization decisions. For example, we are highly dependent on the efforts and expertise of Glaxo in the distribution,
marketing and selling of ENTEREG. Presently, ENTEREG is detailed primarily by Glaxos national hospital-based sales organization. We are co-promoting ENTEREG in certain hospitals with a field force that now numbers approximately 25 persons. The
ultimate commercial success of ENTEREG will depend, to a large degree, on the success of the efforts of Glaxos and our field forces.

We also have a development and commercialization agreement with Pfizer for ADL5859 and ADL5747, our proprietary deltaopioid receptor agonist compounds, for the treatment of pain. Under the Pfizer agreement, we are responsible for
IND filings and Phase 1 and Phase 2a clinical studies and Pfizer is responsible for subsequent worldwide development, securing regulatory approvals and commercialization of the products.

Any failure by our collaborators to perform their obligations or any decision by our collaborators to terminate these agreements under the terms provided
for in their respective agreements could negatively impact our ability to successfully develop, obtain regulatory approvals for and commercialize our product and product candidates, which would likely materially impact our financial condition,
results of operations and our outlook. In addition, any termination of our collaboration agreements will terminate the funding we may receive under the relevant collaboration agreement and may materially and adversely impact our ability to fund
further development efforts and our progress in our development programs.

In the future, we may enter into other collaborative
arrangements for the development, marketing, sale and/or distribution of certain of our product candidates, which may require us to share profits or revenues. For example, we currently have limited marketing, sales and distribution capabilities, and
also have limited resources. Despite our efforts, we may be unable to enter into additional collaborative licensing or other arrangements that we need to develop and commercialize our product candidates. Moreover, we may not realize the contemplated
benefits from such collaborative licensing or other arrangements. These arrangements may place responsibility on our collaborative partners for preclinical testing, human clinical trials, the preparation and submission of



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applications for regulatory approval, or for marketing, sales and distribution support for product commercialization. These arrangements also may require us
to transfer certain material rights or issue our equity securities to corporate partners, licensees or others. Any license or sublicense of our commercial rights may reduce our product revenue. Moreover, we may not derive any revenues or profits
from these arrangements.

We have limited commercial manufacturing capability and expertise, and we rely on third parties to manufacture our products in
sufficient quantities, at an acceptable cost and in compliance with regulatory requirements.

We depend on Piramal Healthcare (Canada)
Limited (formerly Torcan Chemical Ltd.) as the sole approved supplier under our New Drug Application (NDA) of the active pharmaceutical ingredient in ENTEREG. We also depend on Pharmaceutics International, Inc. to manufacture ENTEREG finished
capsules. Changes to our approved suppliers and manufacturers will require FDA approval and could result in delays that disrupt the supply of the product. While we seek to maintain inventory to protect against supply disruptions, if they were to
occur they could materially and adversely affect the commercial success of ENTEREG.

Completion of our clinical trials and
commercialization of our product candidates require access to, or development of, facilities to manufacture a sufficient supply of our product candidates. We have depended, and expect to continue to depend, on third parties for the manufacture of
our product candidates for preclinical, clinical and commercial purposes. We may not be able to contract for the manufacture of sufficient quantities of the products we develop, or even to meet our needs for preclinical or clinical development. Our
products may be in competition with other products for manufacturing capacity of third parties and suitable alternatives may be unavailable. Consequently, our products may be subject to manufacturing delays if outside contractors give their own or
other products greater priority than ours. It is difficult and expensive to change contract manufacturers for pharmaceutical products. Our dependence upon others for the manufacture of our products may adversely affect our future profit margin and
our ability to commercialize products, if additional products are approved, on a timely and competitive basis.

To receive regulatory
approval for a product, our contract manufacturers will be required to obtain approval for their manufacturing facilities to manufacture that product, and there is a risk that such approval may not be obtained. In an NDA, we are required to submit
information and data regarding chemistry, manufacturing and controls which satisfy the FDA that our contract manufacturers are able to make that product in accordance with current Good Manufacturing Practices (cGMPs). Under cGMPs, our manufacturers
and we will be required to manufacture our products and maintain records in a prescribed manner with respect to manufacturing, testing and quality control activities. We are dependent on our third-party manufacturers to comply with these regulations
in the manufacture of our products and these parties may have difficulties complying with cGMPs. The failure of any third-party manufacturer to comply with applicable government regulations could substantially harm and delay or prevent regulatory
approval and marketing of our products.

It is difficult and costly to protect our intellectual property rights, and we cannot ensure the protection of
these rights; we may be sued by others for infringing their intellectual property.

Our commercial success will depend, in part, on
obtaining patent protection for new technologies, products and processes and successfully defending these patents against third-party challenges. To that end, we file applications for patents covering the compositions, uses and proprietary processes
for the manufacture of our product candidates. The patent positions of pharmaceutical and biotechnology companies can be highly uncertain and involve complex legal, scientific and factual questions. Accordingly, we cannot predict the breadth of
claims allowed in our patents or those of our collaborators. The patents and patent applications relating to our products, product candidates and technologies may be challenged, invalidated or circumvented by third parties and might not protect us
against competitors with similar products or technology. Patent disputes in our industry are frequent and can preclude commercialization of products. If we ultimately engage in and lose any such disputes, we could be subject to competition and/or
significant liabilities, we could be required to enter into third-party licenses or we could be required to cease using the technology or product in dispute. In addition, even if such licenses are available, the terms of any license requested by a
third party could be unacceptable to us.

Others have filed, and in the future are likely to file, patent applications covering products
and technologies that are similar, identical or competitive to ours, or important to our business. We cannot be certain that any patent application owned by a third party will not have priority over patent applications filed or in-licensed by us, or
that we or our licensors will not be involved in interference proceedings before U.S. or foreign patent offices.



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Although no third party has asserted a claim of infringement against us, others may hold proprietary
rights that could prevent our product candidates from being marketed unless we can obtain a license to those proprietary rights. Any patent-related legal action against our collaborators or us claiming damages and seeking to enjoin commercial
activities relating to our products and processes could subject us to potential liability for damages and require our collaborators or us to obtain a license to continue to manufacture or market the affected products and processes. We cannot predict
whether our collaborators or we would prevail in any such actions or that any license required under any of these patents would be made available on commercially acceptable terms, if at all.

There has been, and we believe that there will continue to be, significant litigation in the industry regarding patent and other intellectual property
rights. The results of patent litigation among third parties has caused, and may continue to cause, changes to the ways patents are interpreted, enforced and/or challenged. These changes may adversely affect our ability to protect our products. If
we become involved in litigation, it could consume substantial managerial and financial resources.

We also rely on trade secrets to
protect technology in cases when we believe patent protection is not appropriate or obtainable. However, trade secrets are difficult to protect. While we require employees, academic collaborators, consultants and other contractors to enter into
confidentiality agreements, we may not be able to adequately protect our trade secrets or other proprietary information. Our research collaborators and scientific advisors have rights to publish data and information in which we have rights. If we
cannot maintain the confidentiality of our technology and other confidential information in connection with our collaborators and advisors, our ability to receive patent protection or protect our proprietary information may be imperiled.

We are a party to various license agreements that give us rights to use specified technologies in our research and development processes. If we are
not able to continue to license such technology on commercially reasonable terms, our product development and research may be delayed. In addition, we generally do not fully control the prosecution of patents relating to in-licensed technology (or
technology subject to a collaboration) and, accordingly, are unable to exercise the same degree of control over this intellectual property as we exercise over our internally developed technology.

The results and timing of future clinical trials cannot be predicted and future setbacks may materially and adversely affect our business.

We must demonstrate through preclinical testing and clinical trials that a product candidate is safe and efficacious. The results from preclinical
testing and early clinical trials may not be predictive of results obtained in subsequent clinical trials, and we cannot be sure that these clinical trials will demonstrate the safety and efficacy necessary to obtain regulatory approval for any
product candidates.

Many companies in the biotechnology and pharmaceutical industries have suffered significant setbacks in advanced
clinical trials. Product candidates that appear to be promising at earlier stages of development may not reach the market or be marketed successfully for a number of reasons, including, but not limited to, the following:



| |  |  | researchers may find during later preclinical testing or clinical trials that the product candidate is ineffective or has harmful side effects;
| | - |  | -----------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | the number and types of patients available for extensive clinical trials may vary;
| | - |  | ----------------------------------------------------------------------------------



| |  |  | new information about the mechanisms by which a drug candidate works may adversely affect its development;
| | - |  | ----------------------------------------------------------------------------------------------------------



| |  |  | one or more competing products may be approved for the same or a similar condition, raising the hurdles to approval of the product candidate;
| | - |  | ---------------------------------------------------------------------------------------------------------------------------------------------



| |  |  | the product candidate may fail to receive necessary regulatory approval or clearance; or
| | - |  | ----------------------------------------------------------------------------------------



| |  |  | competitors may market equivalent or superior products.
| | - |  | -------------------------------------------------------

The completion of clinical trials of our product candidates may be delayed by many factors, one of which is the rate of enrollment of patients. Neither we nor our collaborators can control the rate at which patients
present themselves for enrollment, and we cannot be sure that the rate of patient enrollment will be consistent with our expectations or be sufficient to enable clinical trials of our product candidates to be completed in a timely manner. In
addition, we often contract with third parties to conduct our clinical trials, and are subject to the risk that these



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third parties fail to perform their obligations properly and in compliance with applicable FDA and other governmental regulations. Any significant delays in,
or termination of, clinical trials of our product candidates may have a material adverse effect on our business.

We cannot be sure that we
will be permitted by regulatory authorities to undertake additional clinical trials for any of our product candidates, or that if such trials are conducted, any of our product candidates will prove to be safe and efficacious or will receive
regulatory approvals. In addition, we, or a regulatory authority, may suspend ongoing clinical trials at any time if the subjects participating in the trial are exposed to unacceptable health risks or if the regulatory agency finds deficiencies in
the conduct of the trials. Any delays in or termination of these clinical trial efforts could have a material and adverse effect on our business.

Our
long-term success depends upon our ability to develop, receive regulatory approval for and commercialize our product candidates and, if we are not successful, our ability to generate revenue from the commercialization of any products resulting from
our development efforts will be limited.

Our product candidates will require governmental approvals prior to commercialization.
Because these product candidates are in development, we face the substantial risks of failure inherent in developing drugs based on new technologies. Our product candidates must satisfy rigorous standards of safety and efficacy before the FDA and
foreign regulatory authorities will approve them for commercial use. There can be no assurance that these standards will remain consistent over time, further complicating our ability to obtain marketing approvals for our product candidates. To
satisfy these standards, we will need to conduct significant additional research, preclinical testing and clinical trials.

Preclinical
testing and clinical development are long, expensive and highly uncertain processes. Failure can occur at any stage of testing. Success in preclinical testing and early clinical trials does not ensure that later clinical trials will be successful.
Based on results at any stage of clinical trials, we may decide to discontinue development of our product candidates. Even if we obtain approval and begin marketing a product, ongoing clinical trials, including for other indications, may result in
additional information that could affect our ability or decision to continue marketing the product. Even if we receive regulatory approval for our product candidates, we must comply with applicable FDA post-marketing regulations governing
manufacturing, promotion, labeling, risk management and reporting of adverse events and other information, as well as other regulatory requirements. Failure to comply with applicable regulatory requirements could subject us to criminal penalties,
civil penalties, recall or seizure of products, withdrawal of marketing approval, total or partial suspension of production or injunction, as well as other regulatory actions against our product or us.

We intend to explore opportunities to expand our product portfolio by acquiring or in-licensing product candidates. Although we conduct extensive
evaluations of product candidate opportunities as part of our due diligence efforts, there can be no assurance that our product candidate development efforts related thereto will be successful or that we will not become aware of issues or
complications that will cause us to alter, delay or terminate our product candidate development efforts.

If we market products in a manner that
violates healthcare fraud and abuse laws, or if we violate government price reporting laws, we may be subject to civil or criminal penalties.

In addition to FDA restrictions on marketing of pharmaceutical products, several other types of state and federal healthcare fraud and abuse laws have been applied in recent years to restrict certain marketing practices in the
pharmaceutical industry. These laws include anti-kickback statutes and false claims statutes. Because of the breadth of these laws and the narrowness of the safe harbors, it is possible that some of our business activities could be subject to
challenge under one or more of these laws.

The federal healthcare program anti-kickback statute prohibits, among other things, knowingly
and willfully offering, paying, soliciting or receiving remuneration to induce, or in return for, purchasing, leasing, ordering or arranging for the purchase, lease or order of any healthcare item or service reimbursable under Medicare, Medicaid or
other federally financed healthcare programs. This statute has been interpreted to apply to arrangements between pharmaceutical manufacturers on the one hand and prescribers, purchasers and formulary managers on the other. Although there are several
statutory exemptions and regulatory safe harbors protecting certain common activities from prosecution, the exemptions and safe harbors are drawn narrowly, and practices that involve remuneration intended to induce prescribing, purchasing or
recommending may be subject to scrutiny if they do not qualify for an exemption or safe harbor. Our practices may not in all cases meet all of the criteria for safe harbor protection from anti-kickback liability.



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Federal false claims laws prohibit any person from knowingly presenting, or causing to be presented, a
false claim for payment to the federal government or knowingly making, or causing to be made, a false statement to get a false claim paid.

Over the past few years, several pharmaceutical and other healthcare companies have been prosecuted under these laws for a variety of alleged promotional and marketing activities, such as: allegedly providing free trips, free goods, sham
consulting fees and grants and other monetary benefits to prescribers; reporting to pricing services inflated average wholesale prices that were then used by federal programs to set reimbursement rates; engaging in off-label promotion that caused
claims to be submitted to Medicaid for non-covered, off-label uses; and submitting inflated best price information to the Medicaid Rebate Program to reduce liability for Medicaid rebates. Most states also have statutes or regulations similar to the
federal anti-kickback law and false claims laws, which apply to items and services reimbursed under Medicaid and other state programs, or, in several states, apply regardless of the payor. Sanctions under these federal and state laws may include
civil monetary penalties, exclusion of a manufacturers products from reimbursement under government programs, criminal fines and imprisonment.

We are required to submit pricing data to the federal government as a condition of selling ENTEREG to healthcare facilities of the Department of Veterans Affairs (VA), the Department of Defense (DoD) and other federal
agencies and having ENTEREG covered under Medicaid. These price reports are used to determine the amount of discounts that must be provided to the VA and DoD healthcare networks. Pharmaceutical manufacturers have been prosecuted under false claims
laws for knowingly submitting inaccurate pricing information to the government to reduce their liability for providing discounts. The rules governing the calculation of these reported prices are complex. We depend upon Glaxo to calculate these
prices for ENTEREG, and it is possible that Glaxos methodologies for calculating these prices could be challenged under false claims laws or other laws. If this were to occur, we could face substantial liability.

We face product liability risks, which may have a negative effect on our financial performance.

The administration of drugs to humans, whether in clinical trials or commercially, can result in product liability claims regardless of whether or not
the drugs are actually at fault for causing an injury. The product labeling for ENTEREG includes a boxed warning that ENTEREG is available only for short-term (15 doses) use in hospitalized patients. The product label informs physicians that there
were more reports of myocardial infarctions in patients treated with alvimopan 0.5 milligrams twice daily compared with placebo-treated patients in a 12-month study of patients treated with opioids for chronic pain. ENTEREG also is marketed and sold
under a REMS.

If ENTEREG is used more widely or if physicians prescribe the product for conditions other than its labeled indication, the
likelihood of an adverse drug reaction, unintended side effect or incident of misuse may increase. Product liability claims can be expensive to defend and may result in large judgments or settlements against us, which could have a negative effect on
our financial performance. The cost of product liability insurance has increased in recent years, and the availability of coverage has decreased. We maintain product liability insurance and self-insurance retentions in amounts we believe to be
commercially reasonable, but which may not cover the potential liability associated with significant product liability claims. Even if a product liability claim is not successful, the adverse publicity and time and expense of defending such a claim
may interfere with our business.

Additionally, we enter into various agreements where we indemnify third parties such as manufacturers and
investigators for certain product liability claims related to our products. These indemnification obligations may require us to pay significant sums of money for claims that are covered by these indemnifications.

Our ability to generate product sales could diminish if we fail to obtain acceptable prices or an adequate level of reimbursement for our products from third-party
payors.

Our ability to successfully commercialize pharmaceutical products, alone or with collaborators, may depend in part on the
extent to which reimbursement is available from government and health administration authorities or private health insurers and third-party payors.

The continuing efforts of government and third-party payors to contain or reduce the costs of healthcare through various means may limit our commercial opportunity. In the United States, we expect that there will continue to be a number of
federal and state proposals to implement pharmaceutical pricing and cost control measures under government healthcare programs such as Medicare and Medicaid. Increasing emphasis on managed care in the United States will continue to put pressure on
the pricing of in-patient hospital procedures and



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pharmaceutical products. Significant uncertainty exists as to the reimbursement status of newly approved healthcare products. Cost control initiatives could
adversely affect the commercialization of our products, decrease the price received for any products in the future and may impede patients ability to obtain reimbursement under their insurance programs for our products.

In the case of partial large or small bowel resection surgery, a hospital typically will be reimbursed a fixed fee for the procedure by a private health
insurer or Medicare. Pharmaceutical products such as ENTEREG that may be used in connection with the surgery are not separately reimbursed and therefore a hospital must assess the cost of ENTEREG relative to its pharmacoeconomic benefit. Current and
future efforts to limit the level of reimbursement for in-patient hospital procedures could cause a hospital to decide to not use ENTEREG or to discontinue use of the product.

If competitors develop and market products that are more effective, have fewer side effects, are less expensive than our product candidates or offer other advantages, our commercial opportunities will be limited.

Other companies have product candidates in development to treat the conditions we are seeking to treat and they may develop effective
and commercially successful products. Our competitors may succeed in developing products that are more effective than those that we may develop, that have fewer side effects, that are less expensive or that they market before we market any products
we may develop.

We are aware of other products in clinical development for the treatment of POI, including methylnaltrexone, which was
developed by Progenics in collaboration with Wyeth. In April 2008, methylnaltrexone as a subcutaneous injection was approved by the FDA for sale in the United States for the treatment of opioid-induced constipation in patients with advanced illness
who are receiving palliative care, when response to laxative therapy has not been sufficient. In addition, Tranzyme Pharma is currently developing TZP-101, an intravenous ghrelin agonist that is currently in Phase 2b clinical testing, for the
treatment of POI and Nektar Therapeutics is currently developing oral NKTR-118, a peripheral opioid antagonist that recently completed Phase 2 clinical testing, for the treatment of opioid induced constipation and other manifestations of OBD. If
Wyeth and Progenics are able to successfully develop methylnaltrexone for the treatment of POI, Tranzyme Pharma is able to successfully develop TZP-101 and/or Nektar is able to successfully develop NKTR-118, our business could be adversely affected.
In addition, there are products already on the market for use in treating other GI conditions that also are being developed for use in opioid induced bowel dysfunction. There may be additional competitive products being developed that could have a
material adverse effect on our ability to successfully market and sell our products.

Our competitors include fully-integrated
pharmaceutical companies and biotechnology companies, universities and public and private research institutions. Many of the organizations competing with us have substantially greater capital resources, larger research and development staffs and
facilities, greater experience in drug development and in obtaining regulatory approvals, and greater manufacturing and marketing capabilities than we do. These organizations also compete with us to:



| |  |  | attract qualified personnel;
| | - |  | ----------------------------



| |  |  | attract partners for acquisitions, joint ventures or other collaborations; and
| | - |  | ------------------------------------------------------------------------------



| |  |  | license proprietary technology.
| | - |  | -------------------------------

Reduction in the
use of opioid analgesics would reduce the potential market for ENTEREG for POI and any products developed to treat OBD.

If the use of
drugs or techniques that reduce the requirement for mu-opioid analgesics becomes more widespread, the market for ENTEREG for POI and our OBD product candidate would decrease. Various techniques to reduce the use of opioids are being utilized
in an attempt to reduce the impact of opioid side effects. The use of local anesthetics in epidural catheters during and after surgery with the continuation of the epidural into the postoperative period can reduce or eliminate the use of opioids.
Non-steroidal anti-inflammatory agents also may reduce total opioid requirements. Continuous infusion of local anesthetic into a wound or near major nerves can reduce the use of opioids in limited types of procedures and pain states. Novel
analgesics that act at receptors other than mu-opioid receptors also are under development. Many companies have developed and are developing analgesic products that compete with opioids or which, if approved, would compete with opioids. If
these analgesics reduce the use of opioids, it would have a negative impact on the potential market for ENTEREG for POI and our OBD product candidate.



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We are or may become involved in legal proceedings that, if adversely adjudicated or settled, could materially impact
our financial condition.

As a public biopharmaceutical company, we are or may become a party to litigation in the ordinary course of
our business, including, among others, matters alleging product liability, patent or other intellectual property rights infringement, patent invalidity, violations of securities laws, employment discrimination or breach of commercial contract. In
general, litigation claims can be expensive and time consuming to bring or defend against and could result in settlements or damages that could significantly impact our results of operations and financial condition.

We have been named in a purported class action lawsuit and related derivative lawsuits. On April 21, 2004, a lawsuit was filed in the U.S. District
Court for the Eastern District of Pennsylvania against us, one of our directors and certain of our officers seeking unspecified damages on behalf of a putative class of persons who purchased Adolor common stock between September 23, 2003 and
January 14, 2004. The complaint alleges violations of Section 10(b) and Section 20(a) of the Securities Exchange Act of 1934, in connection with the announcement of the results of certain studies in our Phase 3 clinical trials for
alvimopan, which allegedly had the effect of artificially inflating the price of our common stock. This suit has been consolidated with three subsequent actions asserting similar claims under the caption In re Adolor Corporation Securities
Litigation, No. 2:04-cv-01728. On December 29, 2004, the District Court issued an order appointing the Greater Pennsylvania Carpenters Pension Fund as Lead Plaintiff. The appointed Lead Plaintiff filed a consolidated amended
complaint on February 28, 2005. That complaint purported to extend the class period, so as to bring claims on behalf of a putative class of Adolor shareholders who purchased stock between September 23, 2003 and December 22, 2004. The
complaint also adds as defendants our Board of Directors asserting claims against them and the other defendants for violation of Section 11 and Section 15 of the Securities Act of 1933 in connection with our public offering of stock in
November 2003. Together with the management and director defendants, we moved to dismiss the complaint on April 29, 2005. The plaintiffs responded to the motion to dismiss on June 28, 2005, and our reply was filed on August 12, 2005.

On August 2, 2004, two shareholder derivative lawsuits were filed in the U.S. District Court for the Eastern District of
Pennsylvania, purportedly on behalf of the Company, against our directors and certain of our officers seeking unspecified damages for various alleged breaches of fiduciary duty and waste. The allegations are similar to those set forth in the class
action complaints, involving the announcement of the results of certain studies in our Phase 3 clinical trials for ENTEREG. On November 12, 2004, the derivative plaintiff filed an amended complaint. On December 13, 2004, we filed a motion
challenging the standing of the derivative plaintiff to file the derivative litigation on our behalf. On December 13, 2004, our directors and officers moved to dismiss the complaint for the failure to state a claim. Plaintiffs responded to
these motions on January 27, 2005 and we filed reply briefs on February 18, 2005.

We have not accrued any amount in our
financial statements as of March 31, 2009 for these matters, and we await the decision of the District Court in each matter.

Our business could
suffer if we are unable to attract, retain and motivate skilled personnel and cultivate key academic collaborations.

We are a small
company, and our success depends on our continued ability to attract, retain and motivate highly-qualified management and scientific personnel. We may not be successful in attracting or retaining qualified individuals. Our success also depends on
our ability to develop and maintain important relationships with leading academic institutions and scientists. Competition for personnel and academic collaborations is intense. In particular, our product development programs depend on our ability to
attract and retain highly-skilled chemists, biologists and clinical development personnel. If we lose the services of any of these personnel, it could impede significantly the achievement of our research and development objectives. In addition, we
will need to hire additional personnel and develop additional academic collaborations as we continue to expand our research and development activities. We do not know if we will be able to attract, retain or motivate personnel or maintain
relationships. We do not maintain key man life insurance on any of our employees.

If we use biological and hazardous materials in a manner that causes
injury or violates laws, we may be liable for damages.

Our research and development activities involve the controlled use of
potentially harmful biological materials as well as hazardous materials, chemicals and various radioactive compounds. We use radioactivity in conducting biological assays and we use solvents that could be flammable in conducting our research and



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development activities. We cannot completely eliminate the risk of accidental contamination or injury from the use, storage, handling or disposal of these
materials. We do not maintain a separate insurance policy for these types of risks. In the event of contamination or injury, we could be held liable for damages that result, and any liability could exceed our resources. We are subject to federal,
state and local laws and regulations governing the use, storage, handling and disposal of these materials and specified waste products. The cost of compliance with these laws and regulations could be significant.

If we engage in an acquisition, reorganization or business combination, we will incur a variety of risks that could adversely affect our business operations or our
stockholders.

From time to time we have considered, and we will continue to consider in the future, strategic business initiatives
intended to further the development of our business. These initiatives may include acquiring businesses, technologies or products or entering into a business combination with another company. If we do pursue such a strategy, we could, among other
things:



| |  |  | issue equity securities that would dilute our current stockholders percentage ownership;
| | - |  | -----------------------------------------------------------------------------------------



| |  |  | incur substantial debt that may place strains on our operations;
| | - |  | ----------------------------------------------------------------



| |  |  | spend substantial operational, financial and management resources in integrating new businesses, technologies and products;
| | - |  | ---------------------------------------------------------------------------------------------------------------------------



| |  |  | assume substantial actual or contingent liabilities; or
| | - |  | -------------------------------------------------------



| |  |  | merge with, or otherwise enter into a business combination with, another company in which our stockholders would receive cash or shares of the other company or a
combination of both on terms that our stockholders may not deem desirable.
| | - |  | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

We are not in a position to predict what, if
any, collaborations, alliances or other transactions may result or how, when or if these activities would have a material effect on us or the development of our business.

Certain provisions of both our charter documents and Delaware law, our adoption of a shareholder rights plan and certain limitations within our collaboration agreements may make an acquisition of us, which may be
beneficial to our stockholders, more difficult.

Provisions of our amended and restated certificate of incorporation and restated
bylaws, as well as provisions of Delaware law, could make it more difficult for a third party to acquire us, even if doing so would benefit our stockholders.

Authorized shares of our common stock and preferred stock are available for future issuance without stockholder approval. The existence of unissued common stock and preferred stock may enable our Board of Directors to
issue shares to persons friendly to current management or to issue preferred stock with terms that could render more difficult or discourage a third-party attempt to obtain control of us by means of a merger, tender offer, proxy contest or
otherwise, which would protect the continuity of our management. In addition, we adopted a shareholder rights plan, the effect of which may be to make an acquisition of us more difficult.

Our amended and restated certificate of incorporation provides for our Board of Directors to be divided into three classes, with the term of one such
class expiring each year, and we have eliminated the ability of our stockholders to consent in writing to the taking of any action pursuant to Section 228 of the Delaware General Corporation Law.

Under our collaboration agreements with Glaxo and Pfizer, there are certain limitations on the ability of Glaxo and Pfizer to acquire our securities.
These limitations make it more difficult for Glaxo or Pfizer to acquire us, even if such an acquisition would benefit our stockholders. The limitations do not prevent Glaxo or Pfizer, among other things, from acquiring our securities in certain
circumstances following initiation by a third party of an unsolicited tender offer to purchase more than a certain percentage of any class of our publicly traded securities.



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



|            |  |                                                                                                                                                                                                
|----------- |  | -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|Exhibit No. |  | Description                                                                                                                                                                                    
|3.1         |  | Amended and Restated Bylaws, effective as of February 24, 2009, filed as Exhibit 3.1 to the Companys Current Report on Form 8-K filed on February 25, 2009.                                   
|            | 
|10.1       |  | Form of Performance-Based Deferred Stock Award dated January 6, 2009, filed as Exhibit 10.1 to the Companys Current Report on Form 8-K filed on January 12, 2009.                             
|            | 
|10.2       |  | Amended and Restated Adolor Corporation Incentive Compensation Plan, effective as of January 2009, filed as Exhibit 10.2 to the Companys Current Report on Form 8-K filed on January 12,
2009.
|            | 
|10.3*       |  | Amendment No. 4, dated as of January 30, 2009, to Collaboration Agreement between Glaxo Group Limited and the Company. (1)                                                                     
|            | 
|31.1*       |  | Certification pursuant to Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.                               
|            | 
|31.2*       |  | Certification pursuant to Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.                               
|            | 
|32.1#       |  | Certification pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.                                                                        
|            | 
|32.2#       |  | Certification pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.                                                                        



|* | Filed herewith.
|- | ---------------

| | Compensation plans and arrangements for executive officers and others.
|- | ----------------------------------------------------------------------

|# | This exhibit shall not be deemed filed for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, or otherwise subject to the liability of that
section. Further, this exhibit shall not be deemed to be incorporated by reference in any document filed under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as amended.
|- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

|(1) | Portions of this Exhibit have been omitted and have been filed separately pursuant to an application for confidential treatment filed with the Securities and Exchange Commission
pursuant to Rule 24b-2 under the Securities Exchange Act of 1934, as amended.
|--- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



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SIGNATURES

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



|                     |  |  |  |                    |  |                                                                                                        
|-------------------- |  |  |  | ------------------ |  | -------------------------------------------------------------------------------------------------------
|                     |  |  |  | ADOLOR CORPORATION
|                     |  |  | 
|Date: April 30, 2009 |  |  |  | By:                |  | /s/ Michael R. Dougherty                                                                               
|                     |  |  |  |                    |  | Michael R. Dougherty                                                                                   
|                     |  |  |  |                    |  | President and Chief Executive Officer                                                                  
|                     |  |  |  |                    |  | (Principal executive officer)                                                                          
|                     |  |  | 
|                     |  |  |  | By:                |  | /s/ Stephen W. Webster                                                                                 
|                     |  |  |  |                    |  | Stephen W. Webster                                                                                     
|                     |  |  |  |                    |  | Senior Vice President, Finance and Chief Financial
Officer (Principal financial and accounting officer)



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