<PAGE>
                                                                   Exhibit 10.13

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER
THE SECURITIES ACT OF 1933, AS AMENDED, OR ANY STATE SECURITIES LAWS, AND MAY
NOT BE SOLD, PLEDGED, OR OTHERWISE TRANSFERRED WITHOUT AN EFFECTIVE
REGISTRATION THEREOF UNDER SUCH ACT AND LAWS OR, SUBJECT TO SECTION 5.3
HEREOF, AN OPINION OF COUNSEL REASONABLY SATISFACTORY TO THE CORPORATION AND
ITS COUNSEL, THAT SUCH REGISTRATION IS NOT REQUIRED.

                           WARRANT TO PURCHASE STOCK

Issuer: Alnylam Pharmaceuticals, Inc., a Delaware corporation
Number of Shares: As set forth below
Class of Stock: Series B Convertible Preferred Stock, $0.0001 par value per
share
Exercise Price: $2.50, subject to adjustment
Issue Date: December 18, 2002
Expiration Date: December 18, 2012

     FOR THE AGREED UPON VALUE of $1.00, and for other good and valuable
consideration, the receipt and sufficiency of which are hereby acknowledged,
this Warrant is issued to SILICON VALLEY BANK (together with its successors and
permitted assigns, "Holder") by Alnylam Pharmaceuticals, Inc., a Delaware
corporation (the "Company").

     Subject to the terms and conditions hereinafter set forth, the Holder is
entitled upon surrender of this Warrant and a duly executed Notice of Exercise
in substantially the form attached hereto as Appendix 1 (the "Notice of
Exercise"), at the principal office of the Company, 790 Memorial Drive, Suite
202, Cambridge, Massachusetts 02139 or such other office as the Company shall
notify the Holder of in writing, to purchase from the Company up to such number
of fully paid and non-assessable shares of the Company's Series B Convertible
Preferred Stock, $0.0001 par value per share (the "Class") as shall equal the
Initial Shares (as defined below) plus the Additional Shares (as defined
below), if any, at a purchase price per Share of Two Dollars Fifty Cents ($2.50)
(the "Exercise Price"). This Warrant may be exercised in whole or in part at
any time and from time to time until 5:00 PM, Eastern time, on the Expiration
Date set forth above, and shall be void thereafter. Until such time as this
Warrant is exercised in full or expires, the Exercise Price and the number of
Shares are subject to adjustment from time to time as hereinafter provided.

     As used herein:

     "Initial Shares" means Twelve Thousand Five Hundred (12,500) shares of the
Class; and

     "Additional Shares" means Twelve Thousand Five Hundred (12,500) shares of
the Class; provided, that this Warrant shall become exercisable for the
Additional Shares, if at all, only from and after such date on or before April
30, 2004, if any, as the total aggregate of Credit Extensions
<PAGE>
(as defined in that certain Loan and Security Agreement of even date herewith
between the Company and Silicon Valley Bank (the "Loan Agreement")) made by
Bank (as defined in the Loan Agreement) first exceed One Million Two Hundred
Fifty Thousand Dollars ($1,250,000.00) regardless of the amount of Obligations
(as defined in the Loan Agreement) outstanding on such date.

     "Shares" means the Initial Shares and the Additional Shares; provided,
that the number of Additional Shares for which this Warrant is or may become
exercisable shall be adjusted from time to time upon the occurrence of one or
more events requiring such adjustment as set forth in this Warrant as if this
Warrant were exercisable for such Additional Shares as of the date of any such
required adjustment.

     Notwithstanding the foregoing definition of Class, upon and after the
automatic or voluntary conversion, redemption or retirement of all (but not less
than all) of the outstanding shares of such Class, including without limitation
the Company's initial registered underwritten public offering and sale of its
securities ("IPO"), then from and after the date upon which all such outstanding
shares have been so converted, redeemed or retired, "Class" shall mean the
Company's Series B-1 Convertible Preferred Stock, $0.0001 par value per share
("Series B-1 Stock") or common stock, $0.0001 par value per share ("Common
Stock"), as applicable, and this Warrant shall be exercisable for such number of
shares of Series B-1 Stock or Common Stock, as the case may be, as shall equal
the number of shares of Series B-1 Stock or Common Stock, as the case may be,
into which the Shares would have been converted pursuant to the Company's
Certificate of Incorporation, as amended, including without limitation the
Certificate of Designation, if any, applicable to the same class or series of
preferred stock as the Shares (the "Certificate") had the Shares been issued and
outstanding immediately prior to such conversion, redemption or retirement, and
the Exercise Price shall be the Series B-1 Stock conversion price or Common
Stock conversion price, as the case may be, as determined pursuant to the
Certificate immediately prior to such conversion, redemption or retirement (all
subject to further adjustment as provided herein).

ARTICLE 1. EXERCISE.

     1.1  Method of Exercise. Holder may exercise this Warrant by delivering
this Warrant together with a duly executed Notice of Exercise to the principal
office of the Company. Unless Holder is exercising the conversion right set
forth in Section 1.2, Holder shall also deliver to the Company a check for the
aggregate Exercise Price for the Shares being purchased.

     1.2  Conversion Right. In lieu of exercising this Warrant as specified in
Section 1.1, Holder may from time to time convert this Warrant, in whole or in
part, into a number of Shares determined as follows:

                         X=Y(A-B)/A
     where:
                         X=the number of Shares to be issued to the Holder.



                                      -2-
<PAGE>

                    Y = the number of Shares with respect to which this Warrant
                    is being exercised.

                    A = the Fair Market Value (as determined pursuant to Section
                    1.3 below) of one Share.

                    B = the Exercise Price.

          1.3  Fair Market Value.

               1.3.1 If shares of the Class (or shares of the Company's stock
into which shares of the Class are convertible or exchangeable) are traded on a
nationally recognized securities exchange or over the counter market, the fair
market value of a Share shall be the closing price of a share of the Class (or
the closing price of a share of the Company's stock for which shares of the
Class are convertible or exchangeable, multiplied by the number of shares of
such stock into which one share of the Class is convertible or exchangeable)
reported for the business day immediately preceding the date of Holder's Notice
of Exercise to the Company, provided that the Company receives such Notice of
Exercise not later than five (5) business days following the date thereof.

               1.3.2 If shares of the Class (or shares of the Company's stock
into which shares of the Class are convertible or exchangeable) are not traded
on a nationally recognized securities exchange or over the counter market, the
Board of Directors of the Company shall determine fair market value in its
reasonable good faith judgment.

          1.4  Delivery of Certificate and New Warrant. Promptly after Holder
exercises or converts this Warrant, the Company at its sole expense shall
promptly deliver to Holder (i) certificates for the Shares acquired upon such
exercise, and (ii) if this Warrant has not been fully exercised or converted and
has not expired, a new warrant of like tenor representing the Shares for which
this Warrant is still exercisable.

          1.5  Replacement of Warrants. On receipt of evidence reasonably
satisfactory to the Company of the loss, theft, destruction or mutilation of
this Warrant and, in the case of loss, theft or destruction, on delivery of an
indemnity agreement reasonably satisfactory in form and amount to the Company
or, in the case of mutilation, on surrender and cancellation of this Warrant,
the Company at its expense shall execute and deliver, in lieu of this Warrant, a
new warrant of like tenor.

          1.6  Assumption on Sale, Merger, or Consolidation of the Company.

               1.6.1 "Acquisition". For the purpose of this Warrant,
"Acquisition" means any sale, assignment, transfer, exclusive license, or other
disposition of all or substantially all of the assets of the Company, or any
acquisition, reorganization, consolidation, or merger of the Company where the
holders of the Company's outstanding voting equity securities immediately prior
to the

                                      -3-


<PAGE>
transaction beneficially own less than a majority of the outstanding voting
equity securities of the surviving or successor entity immediately following
the transaction.

           1.6.2.    Assumption of Warrant.  Upon the closing of any Acquisition
(other than an Acquisition in which the consideration received by the Company's
stockholders consists solely of cash), and as a condition precedent thereto, the
successor or surviving entity shall assume the obligations of this Warrant, and
this Warrant shall be exercisable for the same securities and property as would
be payable for the Shares issuable upon exercise of the unexercised portion of
this Warrant as if such Shares were outstanding on the record date for the
Acquisition and subsequent closing. The Exercise Price shall be adjusted
accordingly, and the Exercise Price and number and class of Shares shall
continue to be subject to adjustment from time to time in accordance with the
provisions hereof.

ARTICLE 2. ADJUSTMENTS TO THE SHARES.

           2.1  Stock Dividends, Splits, Etc.  If the Company declares or pays a
dividend on the outstanding shares of the Class, payable in shares of the Class,
Common Stock or other securities, or subdivides the outstanding shares of the
Class into a greater number of shares of the Class, or subdivides the shares of
the Class in a transaction that increases the amount of Common Stock into which
such shares are convertible, then upon exercise of this Warrant, for each Share
acquired, Holder shall receive, without additional cost to Holder, the total
number and kind of securities to which Holder would have been entitled had
Holder owned the Shares of record as of the date the dividend or subdivision
occurred.

           2.2  Reclassification, Exchange or Substitution.  Upon any
reclassification, exchange, substitution, reorganization or other event that
results in a change of the number and/or class of the securities issuable upon
exercise or conversion of this Warrant, Holder shall be entitled to receive,
upon exercise or conversion of this Warrant, the number and kind of securities
and property that Holder would have received for the Shares if this Warrant had
been exercised immediately before such reclassification, exchange, substitution,
reorganization or other event. The Company or its successor shall promptly issue
to Holder a new warrant of like tenor for such new securities or other property.
The new warrant shall provide for adjustments which shall be as nearly
equivalent as may be practicable to the adjustments provided for in this Article
2 including, without limitation, adjustments to the Exercise Price and to the
number of securities or property issuable upon exercise of the new warrant. The
provisions of this Section 2.2 shall similarly apply to successive
reclassifications, exchanges, substitutions, reorganizations or other events.

           2.3  Adjustments for Combinations, Etc.  If the outstanding shares of
the Class are combined or consolidated, by reclassification or otherwise, into a
lesser number of shares, the Exercise Price shall be proportionately increased
and the number of Shares issuable upon exercise or conversion of this Warrant
shall be proportionately decreased.



                                      -4-



<PAGE>
     2.4  No Impairment. The Company shall not, by amendment of the Certificate
or its by-laws or through a reorganization, transfer of assets, consolidation,
merger, dissolution, issue, or sale of securities or any other voluntary
action, avoid or seek to avoid the observance or performance of any of the
terms to be observed or performed under this Warrant by the Company, but shall
at all times in good faith assist in carrying out of all the provisions of this
Article 2 and in taking all such action as may be necessary or appropriate to
protect Holder's rights under this Article against impairment.

     2.5  Adjustments for Dilutive Issuances. The number of shares of Common
Stock for which the Shares are convertible shall be adjusted from time to time
in accordance with Section 2(e)(iv) of Article Fourth of the Certificate as if
the Shares were issued and outstanding on and as of the date of any such
required adjustment.

     2.6  Fractional Shares. No fractional Shares shall be issuable upon
exercise or conversion of the Warrant and the number of Shares to be issued
shall be rounded down to the nearest whole Share. If a fractional Share
interest arises upon any exercise or conversion of this Warrant, the Company
shall eliminate such fractional Share interest by paying Holder an amount
computed by multiplying such fractional interest by the Fair Market Value
(determined in accordance with Section 1.3 above) of one Share.

     2.7  Certificate as to Adjustments. Upon each adjustment of the Exercise
Price, number or class of Shares or number of shares of Common Stock or other
securities for which the Shares are convertible or exchangeable, the Company at
its expense shall promptly compute such adjustment, and furnish Holder with a
certificate of its chief financial officer setting forth such adjustment and
the facts upon which such adjustment is based. The Company shall at any time
and from time to time, upon written request, furnish Holder with a certificate
setting forth the Exercise Price, number and class of Shares and conversion
ratio in effect upon the date thereof and the series of adjustments leading to
such Exercise Price, number and class of Shares and conversion ratio.

ARTICLE 3. REPRESENTATIONS AND COVENANTS OF THE COMPANY.

     3.1  Representations and Warranties. The Company hereby represents and
warrants to the Holder as follows:

          (a)  All Shares which may be issued upon the due exercise of this
Warrant, and all Common Stock or other securities, if any, issuable upon due
conversion of the Shares, shall, upon issuance, be duly authorized, validly
issued, fully paid and non-assessable, and free of any liens and encumbrances
except for restrictions on transfer provided for herein or under applicable
federal and state securities laws.

          (b)  The Company covenants that it shall at all times cause to be
reserved and kept available out of its authorized and unissued shares such
number of shares of its Series B Convertible Preferred Stock, Series B-1 Stock
and Common Stock and other securities as will be

                                      -5-
<PAGE>
sufficient to permit the exercise in full of this Warrant and the conversion of
the Shares into shares of Series B-1 Stock, Common Stock or such other
securities.

          (c) On and as of the date hereof, (i) $2.50 is the lowest price per
share for which shares of the Class have been sold or issued by the Company, and
the lowest exercise or conversion price per share for which shares of the Class
may be purchased or acquired upon the exercise or conversion of outstanding
securities exercisable or convertible by their terms for shares of the Class,
and (ii) the Common Stock conversion price in effect for shares of the Class as
determined pursuant to the Certificate is $2.50.

          (d) The execution and delivery by the Company of this Warrant and the
performance of all obligations of the Company hereunder, including the issuance
to Holder of the right to acquire the Shares, have been duly authorized by all
necessary corporate action on the part of the Company, and this Warrant is not
inconsistent with the Certificate and/or the Company's by-laws, does not
contravene any law or governmental rule, regulation or order applicable to it,
does not and will not contravene any provision of, or constitute a default
under, any material indenture, mortgage, contract or other instrument to which
it is a party or by which it is bound, and constitutes a legal, valid and
binding agreement of the Company, enforceable in accordance with its terms,
subject to laws of general application relating to bankruptcy, insolvency and
the relief of debtors and the rules or principles of equity governing specific
performance, injunctive relief and other equitable remedies.

     3.2 Notice of Certain Events. If the Company proposes at any time (a)to
declare any dividend or distribution upon outstanding shares of the Class,
whether in cash, property, stock, or other securities and whether or not a
regular cash dividend; (b)to offer for subscription pro rata to the holders of
outstanding shares of the Class any additional shares of stock of any class or
series or other rights; (c)to effect any reclassification or recapitalization of
any of its securities; or (d)to merge or consolidate with or into any other
corporation, or sell, lease, license, or convey all or substantially all of its
assets, or to liquidate, dissolve or wind up; then, in connection with each such
event, the Company shall give Holder(1) at least 10 days prior written notice of
the date on which a record will be taken for such dividend, distribution, or
subscription rights (and specifying the date on which the holders of securities
of the Company shall be entitled to receive such dividend, distribution or
rights) or for determining rights to vote, if any, in respect of the matters
referred to in (c) and (d) above; and (2) in the case of the matters referred to
in (c) and (d) above at lease 10 days prior written notice of the date when the
same will take place (and specifying the date on which the holders of securities
of the Company will be entitled to exchange their securities of the Company for
securities or other property deliverable upon the occurrence of such event).

     3.3 Registration Under Securities Act of 1933, as amended. The Company
grants registration rights to the Holder of this Warrant for any Common Stock
issued and issuable upon exercise hereof or upon conversion of the Shares issued
and issuable hereunder, on the terms and conditions on which registration rights
are granted to the investor parties to that certain Amended and Restated
Registration Rights Agreement dated as of July 25, 2002 among the Company and
the
<PAGE>
other parties listed on Schedule A thereto, as amended and in effect from time
to time (the "Registration Rights Agreement"), provided, however, that the
Holder will have no right to request registration under Section 2 of the
Registration Rights Agreement. Holder hereby agrees to be subject to and bound
by all of the terms and provisions of the Registration Rights Agreement
applicable to the investor parties thereto. The Company represents and warrants
to Holder that the Company's foregoing grant of registration rights (a) has been
duly authorized by all necessary corporate action of the Company's Board of
Directors and shareholders, (b) will not violate the Certificate or the
Company's by-laws, each as amended, (c) will not violate or cause a breach or
default (or an event which with the passage of time or the giving of notice or
both, would constitute a breach or default) under any agreement, instrument,
mortgage, deed of trust or other arrangement to which the Company is a party or
by which it or any of its assets is subject or bound, and (d) does not require
the approval, consent or waiver of or by any shareholder, registration rights
holder or other third party which approval, consent or waiver has not been
obtained as of the date of issuance of this Warrant.

ARTICLE 4. REPRESENTATIONS AND WARRANTIES OF THE HOLDER. Holder represents and
warrants to the Company as follows:

     4.1  Purchase for Own Account. Subject to Silicon Valley Bank's right to
transfer this Warrant and the Shares (and/or the securities, if any, issued and
issuable upon conversion of the Shares) to its parent corporation Silicon
Valley Bancshares and/or any other affiliate, this Warrant and the Shares to be
acquired upon exercise hereof will be acquired for investment for Holders'
account, not as nominee or agent, and not with a view to sale or distribution
in violation of applicable federal and state securities laws.

     4.2  Investment Experience. Holder understands that the purchase of this
Warrant and the Shares covered hereby involves substantial risk. Holder (a) has
experience as an investor in unregistered securities, (b) has sufficient
knowledge and experience in financial and business affairs that it can evaluate
the risks and merits of its investment in this Warrant and the Shares, and (c)
can bear the economic risk of such Holder's investment in this Warrant and the
Shares.

     4.3  Accredited Investor. Holder is an "accredited investor" as such term
is defined in Regulation D under the Securities Act of 1933, as amended (the
"Securities Act").

     4.4  Restricted Securities. Holder understands that this Warrant and the
securities to be issued upon exercise hereof must be held indefinitely unless
subsequently registered under the Securities Act and qualified under any
applicable state securities laws, or unless exemptions from registration and
qualification are otherwise available. Holder is aware of the provision of Rule
144 promulgated under the Securities Act.

ARTICLE 5. MISCELLANEOUS.

     5.1  Intentionally Omitted.

                                      -7-
<PAGE>

          5.2  Legends. This Warrant and the Shares (and the securities
issuable, directly or indirectly, upon conversion of the Shares, if any) shall
be imprinted with a legend in substantially the following form:

     THIS SECURITY HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF
     1933, AS AMENDED, OR ANY STATE SECURITIES LAWS, AND MAY NOT BE SOLD,
     PLEDGED OR OTHERWISE TRANSFERRED WITHOUT AN EFFECTIVE REGISTRATION
     THEREOF UNDER SUCH ACT AND LAWS OR, SUBJECT TO SECTION 5.3 OF THAT
     CERTAIN WARRANT TO PURCHASE STOCK ISSUED BY THE CORPORATION TO SILICON
     VALLEY BANK DATED AS OF DECEMBER 16, 2002, AN OPINION OF COUNSEL
                             -----------------
     REASONABLY SATISFACTORY TO THE CORPORATION AND ITS COUNSEL THAT SUCH
     REGISTRATION IS NOT REQUIRED.

          5.3  Compliance with Securities Laws on Transfer. This Warrant and the
Shares (and the securities, if any, issued and issuable upon conversion of the
Shares) may not be transferred or assigned in whole or in part without
compliance with applicable federal and state securities laws by the transferor
and the transferee (including, without limitation, the delivery of investment
representation letters and legal opinions reasonably satisfactory to the
Company, as reasonably requested by the Company). The Company shall not require
Holder to provide an opinion of counsel if the transfer is to Silicon Valley
Bancshares or other affiliate of Holder.

          5.4  Transfer Procedure. Following its receipt of this executed
Warrant, Silicon Valley Bank will transfer same in whole or in part to its
parent corporation Silicon Valley Bancshares, and thereafter Holder and/or
Silicon Valley Bancshares may, subject to Section 5.3 above, transfer all or
part of this Warrant and/or the Shares (or the securities, if any, issued and
issuable upon conversion of the Shares) at any time and from time to time by
giving the Company notice of the portion of the Warrant and/or Shares (or the
securities, if any, issued and issuable upon conversion of the Shares) being
transferred setting forth the name, address and taxpayer identification number
of the transferee and surrendering this Warrant to the Company for reissuance to
the transferee(s)(and Holder if applicable); provided, that at all times prior
to the Company's IPO, Holder shall not, without the prior written consent of
the Company, transfer this Warrant (or any part hereof), any Shares, or any
securities issued or issuable upon conversion of the Shares, to any person who
directly competes with the Company, unless such transfer is in connection with
an Acquisition of the Company by any such person.

          5.5  Notices. All notices and other communications from the Company to
the Holder, or vice versa, shall be deemed delivered and effective when given
personally, or mailed by first-class registered or certified mail, postage
prepaid, or sent via reputable overnight courier service, fee prepaid, at such
address as may have been furnished to the Company or the Holder, as the case may
be, in writing by the Company or such holder from time to time, but in all
cases, unless instructed in writing otherwise, the Company shall deliver a copy
of all notices to Holder to Silicon Valley Bank, Treasury Department, 3003
Tasman Drive, HA 200, Santa Clara, California 95054.

                                      -8-

<PAGE>

           5.6  Waiver. This Warrant and any term hereof may be changed, waived,
discharged or terminated only by an instrument in writing signed by the party
against which enforcement of such change, waiver, discharge or termination is
sought.

          5.7  Attorneys Fees. In the event of any dispute between the parties
concerning the terms and provisions of this Warrant, the party prevailing in
such dispute shall be entitled to collect from the other party all costs
incurred in such dispute, including reasonable attorneys' fees.

          5.8  Governing Law. This Warrant shall be governed by and construed in
accordance with the laws of The Commonwealth of Massachusetts, without giving
effect to its principles regarding conflicts of law.

          5.9  No Rights as a Shareholder. Except as specifically provided in
this Warrant, Holder shall have no rights as a shareholder of the Company in
respect of the Shares issuable hereunder unless and until Holder exercises this
Warrant as to all or any of such Shares.


                  [REMAINDER OF PAGE LEFT BLANK INTENTIONALLY]

<PAGE>
     IN WITNESS WHEREOF, the Company has caused this Warrant to Purchase Stock
to be executed as an instrument under seal by its duly authorized
representative as of the date first above written.


ATTEST:                                "COMPANY"

                                       ALNYLAM PHARMACEUTICALS, INC.


By: /s/ Jeffrey Wiesen                 By: /s/ John G. Conley
   -----------------------------          ----------------------------------
Name: Jeffrey Wiesen                   Name: John G. Conley
Title: Secretary                       Title: VP, Strategy & Finance



Agreed to and accepted by:

SILICON VALLEY BANK


By: /s/ Douglas Marshall
   -----------------------------
Name: Douglas Marshall
Title: Vice President
<PAGE>
                                   APPENDIX 1


                               NOTICE OF EXERCISE

     1.   The undersigned hereby elects to purchase _______ shares of the
__________ stock of ______________ pursuant to Section 1.1 of the attached
Warrant, and tenders herewith payment of the Exercise Price of such shares in
full.

     1.   The undersigned hereby elects to convert the attached Warrant into
Shares in the manner specified in Section 1.2 of the attached Warrant. This
conversion is exercised with respect to _____________ of shares of the
_______________Stock of _____________________.

     [Strike paragraph that does not apply.]

     2.   Please issue a certificate or certificates representing said shares
in the name of the undersigned or in such other name as is specified below:




                    _________________________________________
                          (Name)




                    _________________________________________


                    _________________________________________
                          (Address)



     3.   The undersigned represents it is acquiring the shares solely for its
own account and not as a nominee for any other party and not with a view toward
the resale or distribution thereof except in compliance with applicable
securities laws.


                                             ___________________________________
                                                   (Signature)

____________________
     (Date)