SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                  Schedule 13G
                                 (Rule 13d-102)

   INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1 (b),
         (c) AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO 13d-2 (b)
                               (Amendment No. 2)*

                          Alnylam Pharmaceuticals, Inc.
                                (Name of Issuer)

                                  Common Stock
                         (Title of Class of Securities)

                                    02043Q107
                                 (CUSIP Number)

                                December 30, 2005
             (Date of Event Which Requires Filing of this Statement)

Check the appropriate box to designate the rule pursuant to which this Schedule
is filed:

[ ]  Rule 13d-1(b)

[ ]  Rule 13d-1(c)

[X]  Rule 13d-1(d)

*    The remainder of this cover page shall be filled out for a reporting
     person's initial filing on this form with respect to the subject class of
     securities, and for any subsequent amendment containing information which
     would alter disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed
to be "filed" for the purpose of Section 18 of the Securities Exchange Act of
1934 ("Act") or otherwise subject to the liabilities of that section of the Act
but shall be subject to all other provisions of the Act (however, see the
Notes).

                         (Continued on following pages)


                                  Page 1 of 16
                            Exhibit Index on Page 13



CUSIP NO. 02043Q107                      13 G                       Page 2 of 16


--------------------------------------------------------------------------------
1    NAME OF REPORTING
     SS OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
        Polaris Venture Partners III, L.P. ("PVP III")

--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*         (a) [ ]   (b) [X]

--------------------------------------------------------------------------------
3    SEC USE ONLY

--------------------------------------------------------------------------------
4    CITIZENSHIP OR PLACE OF ORGANIZATION
     Delaware

--------------------------------------------------------------------------------
                5    SOLE VOTING POWER
                     1,938,532 shares, except that Polaris Venture Management
                     Co. III, L.L.C. ("Polaris III"), the general partner of PVP
                     III, may be deemed to have sole power to vote these shares,
                     and Jonathan A. Flint ("Flint"), Terrance G. McGuire
                     ("McGuire") and Alan G. Spoon ("Spoon"), the managing
                     members of Polaris III, may be deemed to have shared power
                     to vote these shares.

                ----------------------------------------------------------------
  NUMBER OF     6    SHARED VOTING POWER
    SHARES           See response to row 5.
 BENEFICIALLY
OWNED BY EACH   ----------------------------------------------------------------
  REPORTING     7    SOLE DISPOSITIVE POWER
   PERSON            1,938,532 shares, except that Polaris III, the general
    WITH             partner of PVP III, may be deemed to have sole power to
                     dispose of these shares, and Flint, McGuire and Spoon, the
                     managing members of Polaris III, may be deemed to have
                     shared power to dispose of these shares.

                ----------------------------------------------------------------
                8    SHARED DISPOSITIVE POWER
                     See response to row 7.
--------------------------------------------------------------------------------
9    AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
                                                                       1,938,532

--------------------------------------------------------------------------------
10   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES

--------------------------------------------------------------------------------
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
                                                                           7.27%

--------------------------------------------------------------------------------
12   TYPE OF REPORTING PERSON
                                                                              PN
--------------------------------------------------------------------------------



CUSIP NO. 0203Q107                        13 G                      Page 3 of 16


--------------------------------------------------------------------------------
1    NAME OF REPORTING
     SS OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
        Polaris Venture Partners Entrepreneurs' Fund III, L.P. ("Entrepreneurs'
        III")

--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                               (a) [ ]   (b) [X]

--------------------------------------------------------------------------------
3    SEC USE ONLY

--------------------------------------------------------------------------------
4    CITIZENSHIP OR PLACE OF ORGANIZATION
     Delaware

--------------------------------------------------------------------------------
                5    SOLE VOTING POWER
                     50,076 shares, except that Polaris III, the general partner
                     of Entrepreneurs' III, may be deemed to have sole power to
                     vote these shares, and Flint, McGuire and Spoon, the
                     managing members of Polaris III, may be deemed to have
                     shared power to vote these shares.

                ----------------------------------------------------------------
  NUMBER OF     6    SHARED VOTING POWER
    SHARES           See response to row 5.
 BENEFICIALLY
OWNED BY EACH   ----------------------------------------------------------------
  REPORTING     7    SOLE DISPOSITIVE POWER
    PERSON           50,076 shares, except that Polaris III, the general partner
     WITH            of Entrepreneurs' III, may be deemed to have sole power to
                     dispose of these shares, and Flint, McGuire and Spoon, the
                     managing members of Polaris III, may be deemed to have
                     Shared power to dispose of these shares.

                ----------------------------------------------------------------
                8    SHARED DISPOSITIVE POWER
                     See response to row 7.
--------------------------------------------------------------------------------
9    AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
                                                                          50,076

--------------------------------------------------------------------------------
10   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9)
     EXCLUDES CERTAIN SHARES

--------------------------------------------------------------------------------
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
                                                                           0.18%
--------------------------------------------------------------------------------

12   TYPE OF REPORTING PERSON
                                                                              PN
--------------------------------------------------------------------------------



CUSIP NO. 02043Q107                   13 G                          Page 4 of 16


--------------------------------------------------------------------------------
1    NAME OF REPORTING
     SS OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
        Polaris Venture Partners Founders' Fund III, L.P. ("Founders' III")

--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                               (a) [ ]   (b) [X]

--------------------------------------------------------------------------------
3    SEC USE ONLY

--------------------------------------------------------------------------------
4    CITIZENSHIP OR PLACE OF ORGANIZATION
     Delaware

--------------------------------------------------------------------------------
                5    SOLE VOTING POWER
                     30,384 shares, except that Polaris III, the general partner
                     of Founders' III, may be deemed to have sole power to vote
                     these shares, and Flint, McGuire and Spoon, the managing
                     members of Polaris III, may be deemed to have shared power
                     vote these shares.

                ----------------------------------------------------------------
  NUMBER OF     6    SHARED VOTING POWER
    SHARES           See response to row 5.
 BENEFICIALLY
OWNED BY EACH   ----------------------------------------------------------------
  REPORTING
    PERSON      7    SOLE DISPOSITIVE POWER
     WITH            30,384 shares, except that Polaris III, the general partner
                     of Founders' III, may be deemed to have sole power to
                     dispose of these shares, and Flint, McGuire and Spoon, the
                     managing members of Polaris III, may be deemed to have
                     shared power to dispose of these shares.

                ----------------------------------------------------------------
                8    SHARED DISPOSITIVE POWER
                     See response to row 7.
--------------------------------------------------------------------------------
9    AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
                                                                          30,384

--------------------------------------------------------------------------------
10   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9)
     EXCLUDES CERTAIN SHARES

--------------------------------------------------------------------------------
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
                                                                           0.11%

--------------------------------------------------------------------------------
12   TYPE OF REPORTING PERSON
                                                                              PN
--------------------------------------------------------------------------------



CUSIP NO. 02043Q107                    13 G                         Page 5 of 16


--------------------------------------------------------------------------------
1    NAME OF REPORTING
     SS OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
        Polaris Venture Management Co. III, L.L.C. ("Polaris III")

--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                               (a) [ ]   (b) [X]

--------------------------------------------------------------------------------
3    SEC USE ONLY

--------------------------------------------------------------------------------

4    CITIZENSHIP OR PLACE OF ORGANIZATION
     Delaware

--------------------------------------------------------------------------------
                5    SOLE VOTING POWER
                     2,018,992 shares, of which 1,938,532 are directly owned by
                     PVP III, 50,076 are directly owned by Entrepreneurs' III
                     and 30,384 are directly owned by Founders' III. Polaris
                     III, the general partner of PVP III, Entrepreneurs' III and
                     Founders' III, may be deemed to have sole power to vote
                     these shares, and Flint, McGuire and Spoon, the managing
                     members of Polaris III, may be deemed to have shared power
                     to vote these shares.

                ----------------------------------------------------------------
  NUMBER OF     6    SHARED VOTING POWER
   SHARES            See response to row 5.
BENEFICIALLY
OWNED BY EACH   ----------------------------------------------------------------
  REPORTING     7    SOLE DISPOSITIVE POWER
   PERSON            2,018,992 shares, of which 1,938,532 are directly owned by
    WITH             PVP III, 50,076 are directly owned by Entrepreneurs' III
                     and 30,384 are directly owned by Founders' III. Polaris
                     III, the general partner of PVP III, Entrepreneurs' III and
                     Founders' III, may be deemed to have sole power to vote
                     these shares, and Flint, McGuire and Spoon, the managing
                     members of Polaris III, may be deemed to have shared power
                     to dispose of these shares.

                ----------------------------------------------------------------
                8    SHARED DISPOSITIVE POWER
                     See response to row 7.
--------------------------------------------------------------------------------
9    AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
                                                                       2,018,992

--------------------------------------------------------------------------------
10   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9)
     EXCLUDES CERTAIN SHARES

--------------------------------------------------------------------------------
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
                                                                           7.58%

--------------------------------------------------------------------------------
12   TYPE OF REPORTING PERSON
                                                                              OO
--------------------------------------------------------------------------------



CUSIP NO. 02043Q107                    13 G                         Page 6 of 16


--------------------------------------------------------------------------------
1    NAME OF REPORTING
     SS OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
        Jonathan A. Flint ("Flint")

--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                               (a) [ ]   (b) [X]

--------------------------------------------------------------------------------
3    SEC USE ONLY

--------------------------------------------------------------------------------
4    CITIZENSHIP OR PLACE OF ORGANIZATION
     U.S. Citizen

--------------------------------------------------------------------------------
                5    SOLE VOTING POWER
                     0 shares.

                ----------------------------------------------------------------
                6    SHARED VOTING POWER
                     2,018,992 shares, of which 1,938,532 are directly owned by
                     PVP III, 50,076 are directly owned by Entrepreneurs' III
                     and 30,384 are directly owned by Founders' III.
                     Polaris III is the general partner of PVP III,
                     Entrepreneurs' III and Founders' III. Flint is a managing
                     member of Polaris III, and may be deemed to have shared
  NUMBER OF          power to vote these shares.
   SHARES
BENEFICIALLY    ----------------------------------------------------------------
OWNED BY EACH   7    SOLE DISPOSITIVE POWER
  REPORTING          0 shares.
   PERSON
    WITH        ----------------------------------------------------------------
                8    SHARED DISPOSITIVE POWER
                     2,018,992 shares, of which 1,938,532 are directly owned by
                     PVP III, 50,076 are directly owned by Entrepreneurs' III
                     and 30,384 are directly owned by Founders' III. Polaris III
                     is the general partner of PVP III, Entrepreneurs' III and
                     Founders' III. Flint is a managing member of Polaris III,
                     and may be deemed to have shared power to dispose of these
                     shares.
--------------------------------------------------------------------------------
9    AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
                                                                       2,018,992

--------------------------------------------------------------------------------
10   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9)
     EXCLUDES CERTAIN SHARES

--------------------------------------------------------------------------------
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
                                                                           7.58%

--------------------------------------------------------------------------------
12   TYPE OF REPORTING PERSON
                                                                              IN
--------------------------------------------------------------------------------



CUSIP NO. 02043Q107                   13 G                          Page 7 of 16


--------------------------------------------------------------------------------
1.   NAME OF REPORTING
     SS OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
        Terrance G. McGuire ("McGuire")

--------------------------------------------------------------------------------
2.   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                               (a) [ ]   (b) [X]

--------------------------------------------------------------------------------
3.   SEC USE ONLY

--------------------------------------------------------------------------------
4.   CITIZENSHIP OR PLACE OF ORGANIZATION
     U.S.Citizen

--------------------------------------------------------------------------------
                5    SOLE VOTING POWER
                     0 shares.

                ----------------------------------------------------------------
                6    SHARED VOTING POWER
                     2,018,992 shares, of which 1,938,532 are directly owned by
                     PVP III, 50,076 are directly owned by Entrepreneurs' III
                     and 30,384 are directly owned by Founders' III. Polaris III
                     is the general partner of PVP III, Entrepreneurs' III and
                     Founders' III. McGuire is a managing member of Polaris III,
  NUMBER OF          and may be deemed to have shared power to vote these
    SHARES           shares.
 BENEFICIALLY
OWNED BY EACH   ----------------------------------------------------------------
  REPORTING     7    SOLE DISPOSITIVE POWER
    PERSON           0 shares.
     WITH
                ----------------------------------------------------------------
                8    SHARED DISPOSITIVE POWER
                     2,018,992 shares, of which 1,938,532 are directly owned by
                     PVP III, 50,076 are directly owned by Entrepreneurs' III
                     and 30,384 are directly owned by Founders' III. Polaris III
                     is the general partner of PVP III, Entrepreneurs' III and
                     Founders' III. McGuire is a managing member of Polaris III,
                     and may be deemed to have shared power to dispose of these
                     shares.
--------------------------------------------------------------------------------
9    AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
                                                                       2,018,992

--------------------------------------------------------------------------------
10   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9)
     EXCLUDES CERTAIN SHARES

--------------------------------------------------------------------------------
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
                                                                           7.58%

--------------------------------------------------------------------------------
12   TYPE OF REPORTING PERSON
                                                                              IN
--------------------------------------------------------------------------------



CUSIP NO. 02043Q107                   13 G                          Page 8 of 16


--------------------------------------------------------------------------------
1.   NAME OF REPORTING
     SS OR I.R.S. IDENTIFICATION NO. OF ABOVE PERSON
        Alan G. Spoon ("Spoon")

--------------------------------------------------------------------------------
2.   CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                               (a) [ ]   (b) [X]

--------------------------------------------------------------------------------
3.   SEC USE ONLY

--------------------------------------------------------------------------------
4.   CITIZENSHIP OR PLACE OF ORGANIZATION
     U.S.Citizen

--------------------------------------------------------------------------------
                5    SOLE VOTING POWER
                     0 shares.

                ----------------------------------------------------------------
                6    SHARED VOTING POWER
                     2,018,992 shares, of which 1,938,532 are directly owned by
                     PVP III, 50,076 are directly owned by Entrepreneurs' III
                     and 30,384 are directly owned by Founders' III. Polaris III
                     is the general partner of PVP III, Entrepreneurs' III and
                     Founders' III. Spoon is a managing member of Polaris III,
  NUMBER OF          and may be deemed to have shared power to vote these
    SHARES           shares.
 BENEFICIALLY
OWNED BY EACH   ----------------------------------------------------------------
  REPORTING     7    SOLE DISPOSITIVE POWER
    PERSON           0 shares.
     WITH
                ----------------------------------------------------------------
                8    SHARED DISPOSITIVE POWER
                     2,018,992 shares, of which 1,938,532 are directly owned by
                     PVP III, 50,076 are directly owned by Entrepreneurs' III
                     and 30,384 are directly owned by Founders' III. Polaris III
                     is the general partner of PVP III, Entrepreneurs' III and
                     Founders' III. Spoon is a managing member of Polaris III,
                     and may be deemed to have shared power to dispose of these
                     shares.
--------------------------------------------------------------------------------
9    AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
                                                                       2,018,992

--------------------------------------------------------------------------------
10   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9)
     EXCLUDES CERTAIN SHARES

--------------------------------------------------------------------------------
11   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
                                                                           7.58%

--------------------------------------------------------------------------------
12   TYPE OF REPORTING PERSON
                                                                              IN
--------------------------------------------------------------------------------



CUSIP NO. 02043Q107                   13 G                          Page 9 of 16


ITEM 1(A).           NAME OF ISSUER

                     Alnylam Pharmaceuticals, Inc.

ITEM 1(B).           ADDRESS OF ISSUER'S PRINCIPAL EXECUTIVE OFFICES

                     300 Third Street
                     Cambridge, Massachusetts 02142

ITEM 2(A).           NAME OF PERSONS FILING

                     This Statement is filed by Polaris Venture Partners III,
                     L.P., a Delaware limited partnership ("PVP III"), Polaris
                     Venture Partners Entrepreneurs' Fund III, L.P., a Delaware
                     limited partnership ("Entrepreneurs' III"), Polaris Venture
                     Partners Founders' Fund III, L.P., a Delaware limited
                     partnership ("Founders' III"), Polaris Venture Management
                     Co. III, L.L.C., a Delaware limited liability company
                     ("Polaris III"), Jonathan A. Flint ("Flint"), Terrance G.
                     McGuire ("McGuire") and Alan G. Spoon ("Spoon"). Flint,
                     McGuire and Spoon are the managing members of Polaris III.
                     The foregoing entities and individuals are collectively
                     referred to as the "Reporting Persons."

                     Polaris III, the general partner of PVP III, Entrepreneurs'
                     III and Founders' III, may be deemed to have sole power to
                     vote and sole power to dispose of shares of the issuer
                     directly owned by PVP III, Entrepreneurs' III and Founders'
                     III. Flint, McGuire and Spoon are the managing members of
                     Polaris III and may be deemed to have shared power to vote
                     and shared power to dispose of shares of the issuer
                     directly owned by PVP III, Entrepreneurs' III and Founders'
                     III.

ITEM 2(B).           ADDRESS OF PRINCIPAL OFFICE

                     The address for each of the Reporting Persons is:

                     Polaris Venture Partners
                     1000 Winter Street, Suite 3350
                     Waltham, Massachusetts 02451

ITEM 2(C)            CITIZENSHIP

                     PVP III, Entrepreneurs' III and Founders' III are Delaware
                     limited partnerships; Polaris III is a Delaware Limited
                     Liability Company; Flint, McGuire and Spoon are United
                     States citizens.

ITEM 2(D) AND (E).   TITLE OF CLASS OF SECURITIES AND CUSIP NUMBER

                     Common Stock
                     CUSIP # 02043Q107

ITEM 3.              Not Applicable

ITEM 4.              OWNERSHIP

                     The following information with respect to the ownership of
                     the Common Stock of the issuer by the persons filing this
                     Statement is provided as of December 30, 2005:

                          (a)  Amount beneficially owned:

                               See Row 9 of cover page for each Reporting
                               Person.

                          (b)  Percent of Class:



CUSIP NO. 02043Q107                   13 G                         Page 10 of 16


                               See Row 11 of cover page for each Reporting
                               Person.

                          (c)  Number of shares as to which such person has:

                               (i)  Sole power to vote or to direct the vote:

                                    See Row 5 of cover page for each Reporting
                                    Person.

                               (ii) Shared power to vote or to direct the vote:

                                    See Row 6 of cover page for each Reporting
                                    Person.

                               (iii) Sole power to dispose or to direct the
                                    disposition of:

                                    See Row 7 of cover page for each Reporting
                                    Person.

                               (iv) Shared power to dispose or to direct the
                                    disposition of:

                                    See Row 8 of cover page for each Reporting
                                    Person.

ITEM 5.              OWNERSHIP OF FIVE PERCENT OR LESS OF A CLASS.

                     Not applicable.

ITEM 6.              OWNERSHIP OF MORE THAN FIVE PERCENT ON BEHALF OF ANOTHER
                     PERSON.

                     Under certain circumstances set forth in the limited
                     partnership agreements of PVP III, Entrepreneurs' III and
                     Founders' III, the general and limited partners of each of
                     such entities may be deemed to have the right to receive
                     dividends from, or the proceeds from, the sale of shares of
                     the issuer owned by each such entity of which they are a
                     partner.

ITEM 7.              IDENTIFICATION AND CLASSIFICATION OF THE SUBSIDIARY WHICH
                     ACQUIRED THE SECURITY BEING REPORTED ON BY THE PARENT
                     HOLDING COMPANY

                     Not applicable.

ITEM 8.              IDENTIFICATION AND CLASSIFICATION OF MEMBERS OF THE GROUP.

                     Not applicable.

ITEM 9.              NOTICE OF DISSOLUTION OF GROUP.

                     Not applicable.

ITEM 10.             CERTIFICATION.

                     Not applicable.



                                                                   Page 11 of 16


                                   SIGNATURES

          After reasonable inquiry and to the best of my knowledge and belief, I
certify that the information set forth in this statement is true, complete and
correct.

Dated: February 13, 2006


POLARIS VENTURE PARTNERS III, L.P.,     /s/ Kevin Littlejohn
a Delaware Limited Partnership          ----------------------------------------
                                        Signature
                                        Kevin Littlejohn
                                        Authorized Signatory


POLARIS VENTURE PARTNERS                /s/ Kevin Littlejohn
ENTREPRENEURS' FUND III, L.P.,          ----------------------------------------
a Delaware Limited Partnership          Signature
                                        Kevin Littlejohn
                                        Authorized Signatory


POLARIS VENTURE PARTNERS                /s/ Kevin Littlejohn
FOUNDERS' FUND III, L.P.,               ----------------------------------------
a Delaware Limited Partnership          Signature
                                        Kevin Littlejohn
                                        Authorized Signatory


POLARIS VENTURE                         /s/ Kevin Littlejohn
MANAGEMENT CO. III, L.L.C.,             ----------------------------------------
a Delaware Limited Liability Company    Signature
                                        Kevin Littlejohn
                                        Authorized Signatory


JONATHAN A. FLINT                       /s/ Kevin Littlejohn
                                        ----------------------------------------
                                        Signature
                                        Kevin Littlejohn
                                        Authorized Signatory



                                                                   Page 12 of 16


TERRANCE G. MCGUIRE                     /s/ Kevin Littlejohn
                                        ----------------------------------------
                                        Signature
                                        Kevin Littlejohn
                                        Authorized Signatory


ALAN G. SPOON                           /s/ Kevin Littlejohn
                                        ----------------------------------------
                                        Signature
                                        Kevin Littlejohn
                                        Authorized Signatory



                                                                   Page 13 of 16


                                  EXHIBIT INDEX



                                                           Found on Sequentially
Exhibit                                                        Numbered Page
-------                                                    ---------------------
                                                        
Exhibit A: Agreement of Joint Filing                                 14
Exhibit B: Reference to Kevin Littlejohn as
           Authorized Signatory                                      16




                                                                   Page 14 of 16


                                   EXHIBIT A

                            Agreement of Joint Filing

          The undersigned hereby agree that a single Schedule 13G (or any
amendment thereto) relating to the Common Stock of Alnylam Pharmaceuticals, Inc.
shall be filed on behalf of each of the undersigned and that this Agreement
shall be filed as an exhibit to such Schedule 13G.

Dated: February 13, 2006


POLARIS VENTURE PARTNERS III, L.P.,     /s/ Kevin Littlejohn
a Delaware Limited Partnership          ----------------------------------------
                                        Signature
                                        Kevin Littlejohn
                                        Authorized Signatory


POLARIS VENTURE PARTNERS                /s/ Kevin Littlejohn
ENTREPRENEURS' FUND III, L.P.,          ----------------------------------------
a Delaware Limited Partnership          Signature
                                        Kevin Littlejohn
                                        Authorized Signatory


POLARIS VENTURE PARTNERS                /s/ Kevin Littlejohn
FOUNDERS' FUND III, L.P.,               ----------------------------------------
a Delaware Limited Partnership          Signature
                                        Kevin Littlejohn
                                        Authorized Signatory


POLARIS VENTURE                         /s/ Kevin Littlejohn
MANAGEMENT CO. III, L.L.C.,             ----------------------------------------
a Delaware Limited Liability Company    Signature
                                        Kevin Littlejohn
                                        Authorized Signatory


JONATHAN A. FLINT                       /s/ Kevin Littlejohn
                                        ----------------------------------------
                                        Signature
                                        Kevin Littlejohn
                                        Authorized Signatory



                                                                   Page 15 of 16


TERRANCE G. MCGUIRE                     /s/ Kevin Littlejohn
                                        ----------------------------------------
                                        Signature

                                        Kevin Littlejohn
                                        Authorized Signatory


ALAN G. SPOON                           /s/ Kevin Littlejohn
                                        ----------------------------------------
                                        Signature

                                        Kevin Littlejohn
                                        Authorized Signatory



                                                                   Page 16 of 16


                                    EXHIBIT B

              REFERENCE TO KEVIN LITTLEJOHN AS AUTHORIZED SIGNATORY

Kevin Littlejohn has signed the enclosed documents as Authorized Signatory. Note
that copies of the applicable Agreement to File Jointly and Statement Appointing
Designated Filer and Authorized Signatory are already on file with the
appropriate agencies.