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January 12, 2011

By EDGAR Transmission

Securities and Exchange Commission

Division of Corporate Finance

100 F Street, N.E.

Washington, D.C. 20549

Attention: Johnny Gharib

    Re:

    Alnylam Pharmaceuticals, Inc.

Form 10-K

Filed February 26, 2010

File No. 000-50743

Ladies and Gentlemen:

On behalf of Alnylam Pharmaceuticals, Inc. (the “Company”), I am writing in response to comments
contained in the letter dated December 2, 2010 (the “Letter”) from Jeffrey Riedler of the Staff
(the “Staff”) of the Securities and Exchange Commission (the “Commission”) to John M. Maraganore,
the Company’s Chief Executive Officer. The responses set forth below are keyed to the numbering of
the comments and the headings used in the Letter.

Form 10-K, filed February 26, 2010

Business, page 2

    1.

    We note that you have included as exhibits various license agreements with each of Cancer
Research Technology Limited, Carnegie Institution of Washington, Cold Spring Harbor
Laboratory, Garching Innovation GmbH (now known as Max Planck Innovation GmbH) and The Board
of Trustees of the Leland Stanford Junior University. Please describe the material terms of
each of these agreements, including, but not limited to any payment provisions, a range of
royalty rates, aggregate milestones, usage restrictions, exclusivity provisions and duration
and termination provisions.

              Response:

    The Company analyzes each of its agreements for materiality when it enters into
the agreement and periodically thereafter. Item 601(b)(10)(ii)(B) of Regulation S-K
clarifies that if an agreement is such as ordinarily accompanies the kind of business
conducted by the registrant, it will be deemed to be made in the ordinary course of
business, and therefore not required to be filed, unless the agreement is, among other
things, one “upon which the registrant’s business is substantially dependent.” The
Company has reassessed the materiality of its agreements with each of Cancer Research
Technology Limited (“CRT”), Carnegie Institution of Washington

300 Third Street • Cambridge MA, 02142 • main 617.551.8200 • fax 617.551.8101 •

www.alnylam.com

Securities and Exchange Commission

January 12, 2011

Page 2

    (“Carnegie”), Cold Spring Harbor Laboratory (“Cold Spring”) and The Board of
Trustees of the Leland Stanford Junior University (“Stanford”) and concluded
that each such agreement was made in the ordinary course of the Company’s
business and that its business is not currently substantially dependent on
any one of these agreements, and accordingly, the Company does not intend to
continue to file any of these agreements as an exhibit to its Form 10-K for
the year ended December 31, 2010 under Item 601(b)(10) of Regulation S-K.
The Company continues to consider its license agreements with Garching
Innovation GmbH (now known as Max Planck Innovation GmbH) (“Max Planck”)
material agreements. The Company intends to revise its disclosure regarding
the Max Planck license agreements in its Form 10-K for the year ended
December 31, 2010 and to continue to file the agreements as exhibits to its
Form 10-K.

    The Company is a biopharmaceutical company seeking to develop and
commercialize novel therapeutics based on RNA interference (“RNAi”). Patent
protection is critical to success in the research-based biotechnology
industry. Accordingly, license agreements are very much a part of the
ordinary course of business in the industry. As disclosed in its periodic
filings, including its Forms 10-K and 10-Q, part of the Company’s strategy is
to identify and acquire rights to patents and patent applications relevant to
the development of its RNAi therapeutic candidates. As part of this
strategy, the Company has entered into, and intends to continue to enter
into, agreements with respect to a broad portfolio of intellectual property
covering various aspects of RNAi technology. The license agreements with CRT,
Carnegie, Cold Spring and Stanford, pursuant to which the Company has
in-licensed rights to various aspects of RNAi technology, are part of this
ordinary course business strategy.

    In considering the materiality of license agreements for purposes of the
exhibit requirements under Item 601(b)(10) of Regulation S-K, the Company
considers the following factors:

    •

    The impact on the Company’s business (including the Company’s ability
to develop and commercialize RNAi therapeutics and the cost impact) in
the event the license was not available;

    •

    The applicability of the technology to the Company’s drug development
platform and/or drug development strategy;

    •

    The stage of development and value of the therapeutic(s) for which
the technology is relevant and the importance of such technology to the
development and commercialization of such therapeutics; and

    •

    The amount and timing of payments under the license agreement.

Securities and Exchange Commission

January 12, 2011

Page 3

    The Company acknowledges that its business continues to be substantially
dependent on licenses to certain fundamental patents applicable to all small
interfering RNAs (“siRNAs”) and to certain chemistry patents broadly
applicable to siRNAs, including its agreements with Max Planck discussed
below. However, due to the evolution of its patent portfolio and the scope of
the claims contained in certain patents and pending patent applications
covered by the CRT, Carnegie, Cold Spring and Stanford license agreements, as
well as the gradual transition of the Company’s patent portfolio to more
product focused intellectual property, the Company does not currently believe
its business is substantially dependent on these licenses, each of which
represents only a narrow aspect of the Company’s overall patent portfolio.

    The annual aggregate payments that the Company made to CRT, Carnegie, Cold
Spring and Stanford represented less than 1% of the Company’s total operating
expenses in each of 2009 and 2010. In addition, to the extent the Company is
required to make milestone or royalty payments under any of these agreements,
such payments will not represent a material percentage of its operating
expenses or cash, cash equivalents and marketable securities. Accordingly,
the Company does not believe that the payment of development or sales
milestone payments to any of CRT, Carnegie, Cold Spring or Stanford would be
material to the Company’s results of operations or financial condition.

    Notwithstanding the Company’s determination that the CRT, Carnegie, Cold
Spring and Stanford agreements are no longer material under Item 601(b)(10)
of Regulation S-K, the Company believes that disclosure of the patents and
patent applications licensed under the these agreements in its Form 10-K and
other filings provides meaningful information for investors regarding the
Company’s broad intellectual property portfolio.

    In response to the Staff’s comment regarding disclosure of the material terms
of the Max Planck agreements, including, but not limited to any payment
provisions, a range of royalty rates, aggregate milestones, usage
restrictions, exclusivity provisions and duration and termination provisions,
the Company intends to revise its disclosure regarding the Max Planck license
agreements in its Form 10-K for the year ended December 31, 2010 and to
continue to file these agreements as exhibits to its Form 10-K. The revised
disclosure will be substantially similar to that set forth below:

“In December 2002, we entered into a co-exclusive license with Max Planck Innovation (formerly
known as Garching Innovation GmbH) for the worldwide rights to use and sublicense certain patented
technology to develop and commercialize therapeutic products and related applications. We also
obtained the rights to use, without the right to sublicense, the technology for all diagnostic uses
other than for the purposes of therapeutic monitoring. In consideration for the rights to license
this technology, we issued to Max Planck Innovation 723,240 shares of Series B redeemable
convertible preferred stock with a fair value of $1.8 million. We were also given the right to
acquire

Securities and Exchange Commission

January 12, 2011

Page 4

the remaining 50 percent exclusive rights, which right we exercised upon our acquisition of
Ribopharma AG in July 2003. In consideration for the remaining rights to this technology, we
issued Max Planck Innovation an additional 158,605 shares of Series B redeemable convertible
preferred stock with a fair value of $0.4 million. The 881,845 shares of Series B redeemable
convertible preferred stock held by Max Planck Innovation converted into 464,128 shares of common
stock upon the closing of our initial public offering in June 2004.

In June 2005, we entered into an amendment to our agreement with Max Planck Innovation that secured
our exclusivity to use and sublicense certain patented technology to develop and commercialize
therapeutic products and related applications. In connection with this amendment, we issued
270,000 shares of our common stock, which were valued at $2.1 million, to Max Planck Innovation and
certain of its affiliated entities.

We are not obligated to pay any development or sales milestone payments to Max Planck Innovation,
however, we will be required to pay Max Planck Innovation future royalties on net sales of all
therapeutic and prophylactic products developed with the technology, if any.

Our agreements with Max Planck Innovation generally remain in effect until the expiration of the
last-to-expire patent licensed thereunder. We estimate that the principal issued patents covered
under the Max Planck Innovation agreements will expire both in and outside the United States during
2021, subject to any potential patent term extensions, restoration and/or supplemental protection
certificates extending such term extensions in countries where such extensions may become
available. We may terminate the agreements without cause with six months prior notice to Max
Planck Innovation, and Max Planck Innovation may terminate the agreements in the event that we
materially breach our obligations thereunder. Max Planck Innovation also has the right to
terminate the agreements in the event that we, independently or through a third party, attack the
validity of any of the licensed patents.”

Kyowa Hakko Kirin, page 20

    2.

    Please file as an exhibit in your 2010 Form 10-K, the license and collaboration agreement
with Kyowa Hakko Kirin dated June 2008. Alternatively, tell us the basis for your belief that
you are not required to file this agreement pursuant to Item 601(b)(10)(ii)(B) of Regulation
S-K.

              Response:

    As discussed in the Company’s response to Comment No. 1 above, the Company
analyzes each of its agreements for materiality when it enters into the agreement and
periodically thereafter. The Company has determined that its agreement with Kyowa
Hakko Kirin (“Kyowa Hakko”) is not a material contract required to be filed as an
exhibit under Item 601(b)(10) of Regulation S-K. Item 601(b)(10)(ii)(B) of Regulation
S-K clarifies that if an agreement is such as ordinarily accompanies the kind of
business conducted by the registrant, it will be deemed to be made in the ordinary
course of business, and therefore not required to be filed, unless the agreement is,
among other things, one “upon which the registrant’s business is substantially
dependent.” The Company has concluded that its agreement with Kyowa Hakko was made in

Securities and Exchange Commission

January 12, 2011

Page 5

    the ordinary course of the Company’s business and that its business is not
substantially dependent on the agreement, and accordingly, the Company has
not filed this agreement as an exhibit under Item 601(b)(10) of Regulation
S-K.

    The Company is a biopharmaceutical company seeking to develop and
commercialize novel therapeutics based on RNAi. As part of its collaboration
strategy, the Company seeks to enter into 50-50 co-development and/or
worldwide or specific geographic partnerships for specific RNAi therapeutic
programs in the ordinary course of business. Certain of these agreements may
be material to the Company due to a combination of various factors, including
the amount of any upfront payment, the amount of research and development
funding support, the potential future milestone and royalty revenue amounts,
and the geographic scope of the collaboration, among other factors. The Kyowa
Hakko agreement is a regional agreement that provides rights to Kyowa Hakko
to develop and commercialize the Company’s therapeutic candidate, ALN-RSV, at
its own expense in a limited geographic region. Under the Kyowa Hakko
agreement, there are modest development and sales milestone payments and
royalty rates, no co-development obligations, and no obligation on the part
of Kyowa Hakko to provide the Company with development assistance or specific
expertise outside of its limited geographic region.

    The Kyowa Hakko agreement does not fall within any of the enumerated
categories under Item 601(b)(10)(ii)(B) of Regulation S-K that would
disqualify it from the ordinary course exception. Notwithstanding the
Company’s determination that the Kyowa Hakko agreement is not material under
Item 601(b)(10) of Regulation S-K, the Company believes that disclosure of
this agreement in its Form 10-K and other filings provides meaningful
information for investors regarding the Company’s third-party collaboration
efforts.

Delivery Initiatives, page 24

    3.

    We note that during 2007, you obtained an exclusive worldwide license to the liposomal
delivery formulation technology of Tekmira for the discovery, development and
commercialization of LNP formulations for the delivery of RNAi therapeutics, and a
non-exclusive worldwide license to certain liposomal delivery of formulation technology of
Protiva Biotherapeutics Inc., for the discovery, development and commercialization of certain
LNP formulation for the delivery of RNAi therapeutics. Please provide the material terms of
each of these license agreements with Tekmira and Protiva, including, but not limited to any
payment provisions, a range of royalty rates, aggregate milestones, usage restrictions and
duration and termination provisions. Also, please file these agreements as exhibits in your
2010 Form 10-K, or alternatively, tell us the basis for your belief that you are not required
to file these agreements pursuant to Item 601(b)(10)(ii)(B) of Regulation S-K.

Securities and Exchange Commission

January 12, 2011

Page 6

              Response:

    The Company assesses the materiality of each contract it enters into upon signing
and will periodically reassess the materiality of each such agreement as its pipeline
matures and its business changes to determine whether it is reliant on any particular
service, technology or product, or whether any such agreement is otherwise required to
be filed as an exhibit pursuant to the requirements set forth in Item 601(b)(10) of
Regulation S-K. Given the advances of the Company’s clinical pipeline during 2010,
including the initiation of a second clinical development program utilizing the drug
delivery technology covered by the Tekmira and Protiva license agreements, the Company
determined that such agreements are now material to its business. Accordingly, in
response to the Staff’s comment regarding disclosure of the material terms of each of
the Tekmira and Protiva license agreements, including, but not limited to payment
provisions, royalty rates, aggregate milestone payments, usage restrictions and
duration and termination provisions, the Company intends to revise its disclosure
regarding the Tekmira and Protiva license agreements in its Form 10-K for the year
ended December 31, 2010 and to file these agreements as exhibits to its Form 10-K. The
revised disclosure will be substantially