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Correspondence

 Repligen Corporation

 41 Seyon Street, Building #1, Suite 100

 Waltham, Massachusetts 02453

 March 31, 2009

 United States Securities and Exchange
Commission

 Division of Corporation Finance

 100 F Street N.E.

 Washington, D.C. 20549

 Attention:  Jeffrey
Riedler, Assistant Director

RE:

Repligen Corporation

Form 10-K for the Year Ended March 31, 2008

Filed June 13, 2008

File No. 000-14656

 Dear Mr. Riedler:

 This letter is being furnished in response to the comments of the Staff (the “Staff”) of the Securities and Exchange Commission (the “Commission”) in the Commission’s letter dated
March 2, 2009 (the “Comment Letter”) to Dr. Walter C. Herlihy, Ph.D., President, Chief Executive Officer and Director of Repligen Corporation (“Repligen” or the “Company”), with respect to the
Company’s Annual Report on Form 10-K for the fiscal year ended March 31, 2008. The response set forth below has been organized in the same manner in which the Commission’s comments and headings were organized in the Comment Letter.

 Form l0-K for year ended March 31, 2008

 Item 1. Business, page 3

1.
Please file as an exhibit to the Form l0-K the supply agreement between the company and Applied Biosystems, Inc.

 RESPONSE: We respectfully advise the Staff that the Company has not filed the supply agreement with Applied Biosystems, Inc. (“Applied”) because
the Company does not believe that it is a material contract pursuant to Item 601(b)(10) of Regulation S-K. The supply agreement is such as ordinarily accompanies the business of the Company and does not fall into any of the subcategories
contained in Item 601(b)(10)(ii). The supply agreement relates to the sale of Protein A, one of the Company’s products. The supply agreement itself does not obligate Applied to purchase any specific quantity of Protein A from the Company
nor does it obligate the Company to sell any specific quantity of Protein A to Applied. Pursuant to the supply agreement, Applied periodically provides

the Company with a medium term forecast (less than six months) of its need for Protein A on an informational basis, again without a requirement of either
party to buy or sell Protein A. Applied also provides short term forecasts of its Protein A needs, covering a period less than three months. For the first three years of the supply agreement, Applied must buy and the Company must sell Applied 100%
of such short term forecast. For the fourth year of the supply agreement, Applied must buy and the Company must sell to Applied 50% of such short term forecast. The price of such purchases is determined by a matrix set forth in the supply agreement
and is based on volume. While the amount varies from year to year, Applied’s purchases of Protein A from the Company constitute less than 10% of the Company’s product revenues and less than 4% of total revenues. Therefore, the Company does
not believe that the supply agreement with Applied is a material contract required to be filed as an exhibit to its Form 10-K.

2.
We note your discussion in this section of the exclusive license agreement between the company and the Massachusetts Institute of Technology on page 4. Please describe the
material terms of this agreement in this section and file the agreement as an exhibit to the Form 10-K pursuant to Item 60l(b)(10) of Regulation S-K. Alternatively, please provide us with an analysis supporting your determination that the
agreement is not material to the company.

 RESPONSE: We respectfully advise the Staff that the license agreement with the
Massachusetts Institute of Technology (“MIT”) dated May 4, 2004 terminated on the last to expire patents covered by such license. The last to expire patent expired in May 2005. The patents covered by the license were related to the
use of DNA enhancers. Pursuant to the license, the Company was required to pay a certain percentage of any amounts received by the Company from third parties for use of the intellectual property covered by the license. For at least the last 10
years, the technology covered by the license was not relevant to the Company’s core operations. Since May 2005, the license merely acted as a requirement to pay money, if any, upon a successful outcome in the litigation described below.

 Prior to the termination of the License, in May 2004, the Company and MIT sued ImClone Systems, Incorporated (“ImClone”) claiming
infringement of the patents which were the subject of the license. In settlement of such claims, ImClone agreed to pay the Company and MIT $65 million of which approximately $11 million, or 17%, was paid to MIT pursuant to the terms of the license.
The Company has no further obligations or other responsibilities to MIT under this license.

 The Company is currently engaged in the
development and sale, if approved for sale, of (i) Protein A which is used in the manufacture of monoclonal antibodies, (ii) synthetic hormones which, among other things, may assist in the diagnosis of pancreatitis and related disorders,
and (iii) therapeutic product candidates for, among other things, the treatment of bipolar disorder and Friedreich’s ataxia. The Company was incorporated in 1981 and has always been focused, among other things, on the research and
development of therapeutic candidates for various diseases. The Company has frequently in-licensed various technologies and inventions, including those covered by patents. The in-license

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of patents is one that ordinarily accompanies the business of researching and developing therapeutic product candidates as contemplated by
Item 601(b)(10) of Regulation S-K and does not fall into any of the subcategories contained in Item 601(b)(10)(ii). In addition, all patent rights under the license have expired and no further payments are due under the license. Therefore,
the Company does not believe the license from MIT is a material contract required to be filed as an exhibit to its Form 10-K.

3.
We note your discussion of the exclusive license agreement between the company and the University of Michigan on page 4, which agreement has been filed as a material contract and
incorporated by reference to your 10-K. Please describe the material terms of the agreement in this section of the 10-K.

 RESPONSE: We respectfully advise the Staff that we propose to include in the Company’s annual report on Form 10-K for the year ended March 31, 2009, the following disclosure regarding the material terms of the license agreement
with the University of Michigan. All proposed changes to such disclosure compared to previously submitted disclosures in our annual report on Form 10-K for the year ended March 31, 2008 to incorporate the Staff’s recommendations are
highlighted in bold italic print:

 “CTLA4-Ig

 CTLA4 is a key regulator of the activity of the immune system. CTLA4 “turns off” the immune system after it has successfully cleared a bacterial
or viral infection by blocking the activation of T-cells, the immune cells responsible for initiating an immune response. In the 1990’s, our collaborators at the University of Michigan and the U.S. Navy demonstrated in animal models that a
fusion protein consisting of fragments of CTLA4 and an antibody (“CTLA4-Ig”) could be used to treat certain autoimmune diseases. This research finding resulted in the granting of U.S. patent No. 6,685,941 (“the ‘941
Patent”) covering the treatment of certain auto-immune disorders including rheumatoid arthritis with CTLA4-Ig. The ‘941 Patent is owned by the University of Michigan and exclusively licensed to Repligen. In consideration of this
exclusive license, Repligen agreed to pay the University of Michigan 15% of all royalty income received, after deducting legal expenses. CTLA4-Ig’s mechanism of action is different from the current therapies for autoimmune disease or
organ transplant rejection, thus it may provide a treatment for patients who are refractory to existing therapies.

 In December 2005, the FDA approved Bristol’s application to market CTLA4-Ig, under the brand name Orencia®, for treatment of rheumatoid arthritis. In
January 2006, Repligen and the University of Michigan jointly filed a lawsuit against Bristol in the United States District Court for the Eastern District of Texas for patent infringement. In April 2008, Repligen and the University of Michigan
entered into a settlement agreement with Bristol pursuant to which, Bristol made an initial payment of $5 million to Repligen and will pay us royalties on the U.S. net sales of Orencia® for
any clinical indication at a rate of 1.8% for the first $500 million of annual sales, 2.0% for the next $500 million and 4% of annual sales in excess of $1 billion for each year from January 1, 2008 until December 31, 2013.”

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4.
We note your discussion of the settlement agreement between the company and Bristol-Myers Squibb on pages 4, 6 and 55. Please file this agreement as an exhibit to the Form l0-K
pursuant to Item 60l(b)(10) of Regulation S-K.

 RESPONSE: We respectfully advise the Staff that the Settlement and
Release Agreement between the Company, the Regents of the University of Michigan and Bristol-Myers Squibb Company was executed and became effective on April 7, 2008 (the “Bristol Agreement”), after the end of our fiscal year 2008
which ended on March 31, 2008. Item 601(a)(4) of Regulation S-K requires the Company to file as exhibits to Form 10-K material contracts, pursuant to Item 601(b)(10), a material contract which is executed or becomes effective during
the reporting period reflected by the Form 10-Q or Form 10-K. Since the Bristol Agreement was executed after the reporting period reflected in the Form 10-K it was not filed as an exhibit thereto. We advise the Staff that the execution of the
Bristol Agreement was disclosed pursuant to Item 1.01 of a Form 8-K which was filed on April 11, 2008 and the Bristol Agreement itself was filed as Exhibit 10.1 to the Company’s Form 10-Q for the three month period ending
June 30, 2008 which was filed on August 8, 2008. We further advise the Staff that we intend to incorporate by reference the Bristol Agreement as an exhibit to the Company’s Form 10-K for the year ending March 31, 2009 as required
by Item 601 of Regulation S-K.

 Item 5. Market for Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of
Equity Securities, page 14

5.
Please revise to disclose the information required by Item 201(e) of Regulation S-K.

 RESPONSE: We respectfully advise the Staff that pursuant to Instruction 7 to Item 201(e), the Company has included the performance graph required by
Item 201(e) of Regulation S-K in an annual report to security holders required by Exchange Act Rule 14a-3 (the “2008 Annual Report”) that accompanied the registrant’s proxy relating to the Company’s 2008 annual meeting of
security holders at which directors were to be elected. Pursuant to Rule 14a-3(b)(9), the performance graph required by Item 201(e) of Regulation S-K is required to be included in an annual report to shareholders. In lieu of providing
shareholders with the Company’s Annual Report on Form 10-K in satisfaction of the requirements of Rule 14a-3, the Company delivered the 2008 Annual Report which met the conditions required therein. As required by Rule 14a-3(c), seven copies of
the Company’s 2008 Annual Report were filed with the Commission. For our 2009 annual report to shareholders, we intend to include the performance graph as we did in the 2008 Annual Report.

 Notes to Consolidated Financial Statements

 11. Scripps
Agreement, page 54

6.
 You state that, pursuant to the company’s license agreement with The Scripps Research Institute, Repligen has agreed to make certain additional payments in
the event it achieves specified developmental and commercial milestones. Notwithstanding that the

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company has been granted confidential treatment for portions of this agreement, including the amount of specific potential milestone payments, please
disclose the aggregate potential milestone payments to be made under the agreement, Alternatively, please provide your analysis why these aggregate potential payments are not material.

 RESPONSE: We respectfully agree with the Staff’s recommendation that further disclosure of the aggregate potential milestone payments is appropriate.
In response to the Staff’s comment, we would have made the following revised disclosure as of March 31, 2008 and are planning to include equivalent disclosure in our future filings on form 10-K. We have included the first two paragraphs of
the related disclosure as of March 31, 2008 below for reference. All proposed changes or additions to such disclosure to incorporate the Staff’s recommendations are highlighted in bold italic print:

 “11. Scripps Agreements

 License Agreement

 On April 6, 2007 (“the Effective Date”), the Company entered into an
exclusive worldwide commercial license agreement (“License Agreement”) with The Scripps Research Institute (“Scripps”). Pursuant to the License Agreement, the Company obtained a license to use, commercialize and sublicense
certain patented technology and improvements thereon, owned or licensed by Scripps, relating to compounds which may have utility in treating Friedreich’s Ataxia, an inherited neurodegenerative disease. Research in tissues derived from patients,
as well as in mice, indicates that the licensed compounds increase production of the protein frataxin, which suggests potential utility of these compounds in slowing or stopping progression of the disease. There are currently no approved treatments
for Friedreich’s ataxia.

 Pursuant to the License Agreement, the Company agreed to pay Scripps an initial license fee
of $300,000, certain royalty and sublicense fees and, in the event the Company achieves specified developmental and commercial milestones, certain additional milestone payments. Total future milestone payments, were all milestones to be
achieved, would be approximately $4.3 million. In addition, the Company issued Scripps and certain of its designees 87,464 shares of the Company’s common stock (the “Shares”) representing $300,000 as of the Effective Date. The
Company recorded the initial license payment and the value of the shares issued as research and development costs in the Company’s statement of operations in fiscal 2008.”

 Definitive Proxy Statement

 Compensation Discussion and Analysis, page 18

7.
 We note your statements on page 18 that the Compensation Committee set total executive officer compensation in fiscal 2008 based on the Radford Biotechnology
Survey. Please revise your discussion to identify the companies from the survey that were reviewed by

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the Compensation Committee and used as a basis for the salaries paid to Repligen’s executive officers. If the companies are too numerous to list,
please disclose the criteria for including these companies in the Survey.

 RESPONSE: We respectfully agree with the
Staff’s recommendation that further identification of the criteria used for inclusion in the Radford Biotechnology Survey is appropriate. In response to the Staff’s comment, we would have revised our Definitive Proxy Statement and are
planning to include equivalent disclosure in future filings as appropriate. We have included the first two paragraphs of the related disclosure as of March 31, 2008 below for reference. All proposed changes or additions to such disclosure to
incorporate the Staff’s recommendations are highlighted in bold italic print:

 “Executive Compensation

 Base Salary. Each executive officer (except the Chief Executive Officer whose performance is reviewed by the
Compensation Committee) has an annual performance review with the Chief Executive Officer, who makes recommendations on salary increases, promotions and equity grants to the Compensation Committee. The recommended salary increases are based on the
executive officer’s qualifications, performance, experi