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February 18, 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 February 11, 2011 (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 your response to our prior comment 1 and your disclosure regarding your license
agreement with Max Planck Innovation that you will be required to pay future royalties on net
sales of all therapeutic and prophylactic products. Please revise your disclosure to include
a range of royalty rates not to exceed ten percent. An acceptable range of royalties is one
of the following: “single-digits,” “teens,” “twenties,” etc.

    Response:

    In response to the Staff’s comment, the Company has revised its disclosure
regarding its license agreement with Max Planck Innovation to include a range of
royalty rates. The Company intends to include revised disclosure in its Form 10-K for
the year ended December 31, 2010 substantially similar to that set forth below:

“In December 2002, we entered into a co-exclusive license with Max Planck Innovation 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

Page 2

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 the remaining 50% 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
single-digit 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.

    We note your response to our prior comment 2 that under the Kyowa Hakko Kirin agreement,
there are modest development and sales milestone payments and royalty rates. However, we also
note in your 2009 Form 10-K that Kyowa Hakko Kirin paid you an upfront cash payment of $15
million and is required to make payments to you upon achievement of specified development
sales milestones totaling up to $78 million in addition to royalty payments based on annual
net sales. These amounts do not appear to be modest given that you had revenues of
approximately $100 million and net losses of approximately $47.6 million in 2009. Please file
as an exhibit to your 2010 Form 10-K, the license and collaboration agreement with Kyowa Hakko
Kirin dated June 2008.

    Response:

    The Company acknowledges the Staff’s comment and intends to file the license and
collaboration agreement with Kyowa Hakko Kirin as an exhibit to its Form 10-K for the
year ended December 31, 2010.

Page 3

Delivery Initiatives, page 24

    3.

    We note your response to our prior comment 3 and your disclosure that Tekmira and Protiva are
eligible to receive royalty payments on annual product sales of each RNAi therapeutic
formulated using Tekmira’s or Protiva’s liposomal delivery formulation technologies, and that
you are eligible to receive royalties on annual sales of RNAi therapeutic products for which
you granted Tekmira and Protiva licenses. Please revise your disclosure to include a range of
royalty rates not to exceed ten percent for royalties that you will pay to and receive from
Tekmira and Protiva. An acceptable range of royalties is one of the following:
“single-digits,” “teens,” “twenties,” etc.

    Response:

    In response to the Staff’s comment, the Company has revised its disclosure
regarding its license agreements with Tekmira and Protiva to include a range of royalty
rates. The Company intends to include revised disclosure in its Form 10-K for the year
ended December 31, 2010 substantially similar to that set forth below:

“In January 2007, we 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 formulation technology of Protiva Biotherapeutics Inc., or Protiva, for the discovery,
development and commercialization of certain LNP formulations for the delivery of RNAi
therapeutics. In May 2008, Tekmira acquired Protiva. In connection with this acquisition, we
entered into new agreements with Tekmira and Protiva, which provide us access to key existing and
future technology and intellectual property for the systemic delivery of RNAi therapeutics with
liposomal delivery technologies. Under these agreements, we continue to have exclusive rights to
the Semple (U.S. Patent No. 6,858,225) and Wheeler (U.S. Patent Nos. 5,976,567 and 6,815,432)
patents for RNAi, which we believe are critical for the use of LNP delivery technology. Under our
agreements with Tekmira and Protiva, Tekmira and Protiva are eligible to receive up to an aggregate
of $16.0 million in milestone payments for each RNAi therapeutic formulated using Tekmira’s or
Protiva’s liposomal delivery formulation technologies, together
with single-digit royalty
payments on annual product sales. In each of 2009 and 2010, we paid $0.5 million in milestone
payments to Tekmira under these license agreements. We charge these milestone payments to research
and development expense.

We are developing ALN-VSP, a systemically delivered RNAi therapeutic, for the treatment of primary
and secondary liver cancer. ALN-VSP contains two siRNAs formulated using a first-generation LNP
formulation developed by Tekmira. We also have rights to use this LNP technology in the advancement
of our other systemically delivered RNAi therapeutic programs, and we are advancing ALN-TTR01, for
the treatment of ATTR, utilizing this first-generation LNP formulation. In parallel with ALN-TTR01,
we are advancing ALN-TTR02 utilizing a second-generation LNP formulation. In addition, we have
published pre-clinical results from development programs for other systemically delivered RNAi
therapeutics, including ALN-PCS, for the treatment of severe hypercholesterolemia. We are also
advancing ALN-PCS using a second-generation LNP formulation.

Page 4

Under our agreements with Tekmira and Protiva, we also granted Tekmira and Protiva three exclusive
and five non-exclusive licenses under our InterfeRx program to develop and commercialize RNAi
therapeutics directed to up to eight gene targets in which we have no direct strategic interest,
including the targets apolipoprotein B and polo-like kinase 1, or PLK1, and a recently granted
license in connection with Tekmira’s research program directed towards the Ebola virus. We are
eligible to receive up to an aggregate of $8.5 million in milestone payments for each RNAi
therapeutic directed to four of these targets, together with
single-digit royalties on
annual sales of RNAi therapeutic products directed to all of these targets, if any. In addition,
under our agreement with Protiva, we have the right to “opt-in” to the Tekmira research program
directed to PLK1 and contribute 50% of product development costs and share equally in any future
product revenues. We have until the start of a Phase II clinical trial in this PLK1 research
program to exercise our opt-in right.

In connection with Tekmira’s acquisition of Protiva, in May 2008, we made an equity investment of
$5.0 million in Tekmira, purchasing 2,083,333 shares of Tekmira common stock at a price of $2.40
per share, which represented a premium of $1.00 per share. In November 2010, Tekmira effected a
one-for-five reverse stock split, after which we own 416,666 shares of Tekmira common stock.

The terms of our agreements with Tekmira and Protiva generally end upon the expiration of the
last-to-expire patent licensed thereunder, whether such patent is a patent licensed by Tekmira or
Protiva to us, or vice versa. As the licenses from Tekmira and Protiva will include additional
patents, if any, filed to cover future inventions, if any, the dates of expiration cannot be
determined at this time. Either we or Protiva may terminate a license it granted to the other in
the event that the other party materially breaches its obligations relating to that license.
Furthermore, either we or Tekmira may terminate our agreements with each other in the event the
other party materially breaches an obligation under those agreements, but such termination will be
limited to a particular product and/or region in the event of a material breach by the other party
that has a material adverse effect only on that particular product in that region.”

Proxy Statement on Schedule 14A, filed April 20, 2010

2009 Annual Incentive Program, page 26

    4.

    We note your response to our prior comment 5 and your disclosure regarding 2010 corporate
goals and individual objectives. We also note your discussion of Ms. Allen’s individual
objectives which are partly focused on meeting specified financial goals, including meeting
specified operating expense levels and minimum cash balance requirements at year-end. These
objectives appear to be quantitative. To the extent that the objectives are quantitative,
please revise your disclosure so that the discussion of objectives and achievements is also
quantitative.

    Response:

    In response to the Staff’s comment, the Company has revised the
disclosure regarding Ms. Allen’s individual objectives to include a
quantitative discussion of the minimum year-end cash requirements. The Company
has not disclosed Ms. Allen’s performance target with respect to specified
internal operating expense levels under its annual operating plan because the
Company believes that this information constitutes confidential financial data, the
disclosure of which would result in competitive harm to it. Each year, the Company
engages in a robust process to establish the operating plan, which contains financial
targets and budgets that are used to guide the operations of the Company. In
developing the operating plan, management considers various factors relating to
its own operations and research and development programs, as well as overall
economic and market conditions. The operating plan is prepared by Company management
and presented to the Board of Directors (the “Board”) for its consideration
and the Board provides feedback to management.

Page 5

    The finalized operating plan that results from this process is then approved by the
Board. The Company has included disclosure that Ms. Allen’s target specified operating
expense levels for 2010 were set at a level that was attainable but difficult to achieve.
The Company intends to include revised disclosure regarding Ms. Allen’s individual
objectives and performance in its 2011 proxy statement substantially similar to that set forth below:

“Ms. Allen’s individual objectives were
focused on meeting specified financial goals, including meeting specified internal operating expense
levels under our annual operating plan within 5% of target, which we believe were set at
levels that were attainable but aggressively established, and year-end minimum cash balance
requirements of greater than $340.0 million (excluding a potential one-time license payment from a collaborator)
([  ]%), supporting business development efforts to establish strategic alliances to fund our
business ([  ]%), managing our investment portfolio ([  ]%) and managing the audit of our financial
statements, along with various public reporting obligations and tax matters ([  ]%), and achieving
specified metrics with respect to the information technology and facilities groups ([  ]%). Our
compensation committee also considered both Dr. Maraganore’s and Mr. Greene’s recommendations with
respect to Ms. Allen’s performance.  Our compensation committee determined that Ms. Allen achieved [  ]%
of her individual objectives for 2010, including meeting specified year-end internal operating expense
levels under our annual operating plan and achievement of internal year-end cash balance objectives
of greater than $340.0 million, ending 2010 with $350.0 million.  Our compensation committee determined
that under the 2010 annual incentive program, Ms. Allen earned a cash incentive award of $[  ],
representing [  ]% of her target cash award opportunity, reduced by
the corporate performance modifier of [  ]%.”

If you require additional information, please telephone either the undersigned at (617) 551-8200,
or Lia Der Marderosian of WilmerHale, the Company’s outside counsel, at (617) 526-6000.

Very truly yours,

/s/ Patricia L. Allen

Patricia L. Allen

Vice President of Finance and Treasurer

    cc:

    Philip T. Chase, Esq.

Lia Der Marderosian, Esq.