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                                                                    Exhibit 10.4




                          ALNYLAM PHARMACEUTICALS, INC.

                        2004 EMPLOYEE STOCK PURCHASE PLAN

      The purpose of this Plan is to provide eligible employees of Alnylam
Pharmaceuticals, Inc., a Delaware corporation (the "Company"), and certain of
its subsidiaries with opportunities to purchase shares of the Company's common
stock, $.0001 par value (the "Common Stock"). An aggregate of 600,000 shares of
Common Stock have been approved for this purpose. This Plan is intended to
qualify as an "employee stock purchase plan" as defined in Section 423 of the
Internal Revenue Code of 1986, as amended (the "Code"), and the regulations
promulgated thereunder, and shall be interpreted consistent therewith.

      1. Administration. The Plan will be administered by the Company's Board of
Directors (the "Board") or by a Committee appointed by the Board (the
"Committee"). The Board or the Committee has authority to make rules and
regulations for the administration of the Plan and its interpretation and
decisions with regard thereto shall be final and conclusive.

      2. Eligibility. All employees of the Company and all employees of any
subsidiary of the Company (as defined in Section 424(f) of the Code) designated
by the Board or the Committee from time to time (a "Designated Subsidiary"), are
eligible to participate in any one or more of the offerings of Options (as
defined in Section 9) to purchase Common Stock under the Plan provided that:

                  (a) they are customarily employed by the Company or a
      Designated Subsidiary for more than twenty (20) hours a week and for more
      than five (5) months in a calendar year; and

                  (b)   they have been employed by the Company or a
      Designated Subsidiary for at least six (6) months prior to enrolling in
      the Plan;

                  (c)   they are employees of the Company or a Designated
      Subsidiary on the first day of the applicable Plan Period (as defined
      below); and

                  (d) in the case of an executive officer of the Company or a
      Designated Subsidiary, they are not considered a "highly compensated
      individual" within the meaning of Section 414(q) of the Code.

      No employee may be granted an option hereunder if such employee,
immediately after the option is granted, owns 5% or more of the total combined
voting power or value of the stock of the Company or any subsidiary. For
purposes of the preceding sentence, the attribution rules of Section 424(d) of
the Code shall apply in determining the stock ownership of an employee, and all
stock which the employee has a contractual right to purchase shall be treated as
stock owned by the employee.

      3. Offerings. The Company will make one or more offerings ("Offerings") to
employees to purchase stock under this Plan. Offerings will begin each November
1 or the first


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business day thereafter (the "Offering Commencement Dates"). Each Offering
Commencement Date will begin a twelve-month period (a "Plan Period") during
which payroll deductions will be made and held for the purchase of Common Stock
at the end of the Plan Period. The Board or the Committee may, at its
discretion, choose a different Plan Period of twelve (12) months or less for
subsequent Offerings. Notwithstanding anything to the contrary, the first Plan
Period shall begin on the later of November 1, 2004 or the first date that the
Common Stock is publicly traded following the Company's IPO (the "IPO Date"),
and shall end on October 31, 2005.

      4. Participation. An employee eligible on the Offering Commencement Date
of any Offering may participate in such Offering by completing and forwarding a
payroll deduction authorization form to the employee's appropriate payroll
office at least five (5) business days prior to the applicable Offering
Commencement Date. The form will authorize a regular payroll deduction from the
Compensation received by the employee during the Plan Period. Unless an employee
files a new form or withdraws from the Plan, his deductions and purchases will
continue at the same rate for future Offerings under the Plan as long as the
Plan remains in effect. The term "Compensation" means the amount of money
reportable on the employee's Federal Income Tax Withholding Statement, excluding
overtime, shift premium, incentive or bonus awards, allowances and
reimbursements for expenses such as relocation allowances for travel expenses,
income or gains on the exercise of Company stock options or stock appreciation
rights, amounts imputed in respect of benefit programs and similar items,
whether or not shown on the employee's Federal Income Tax Withholding Statement,
but including, in the case of salespersons, sales commissions to the extent
determined by the Board or the Committee.

      5. Deductions. The Company will maintain payroll deduction accounts for
all participating employees. With respect to any Offering made under this Plan,
an employee may authorize a payroll deduction in any dollar amount up to a
maximum of 15% of the Compensation he or she receives during the Plan Period or
such shorter period during which deductions from payroll are made. Payroll
deductions may be at the rate of 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%,
12%, 13%, 14% or 15% of Compensation with any change in compensation during the
Plan Period to result in an automatic corresponding change in the dollar amount
withheld. The minimum payroll deduction is such percentage of compensation as
may be established from time to time by the Board or the Committee.

      6. Deduction Changes. An employee may decrease or discontinue his payroll
deduction once during any Plan Period, by filing a new payroll deduction
authorization form. However, an employee may not increase his payroll deduction
during a Plan Period. If an employee elects to discontinue his payroll
deductions during a Plan Period, but does not elect to withdraw his funds
pursuant to Section 8 hereof, funds deducted prior to his election to
discontinue will be applied to the purchase of Common Stock on the Exercise Date
(as defined below).

      7. Interest. Interest will not be paid on any employee accounts.

      8. Withdrawal of Funds. An employee may at any time prior to the close of
business on the last business day in a Plan Period and for any reason
permanently draw out the balance accumulated in the employee's account and
thereby withdraw from participation in an Offering. Partial withdrawals are not
permitted. The employee may not begin participation again during



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the remainder of the Plan Period. The employee may participate in any subsequent
Offering in accordance with terms and conditions established by the Board or the
Committee.

      9. Purchase of Shares. On the Offering Commencement Date of each Plan
Period, the Company will grant to each eligible employee who is then a
participant in the Plan an option ("Option") to purchase on the last business
day of such Plan Period (the "Exercise Date"), at the Option Price hereinafter
provided for, the largest number of whole shares of Common Stock of the Company
as does not exceed the number of shares determined by multiplying $2,083 by the
number of full months in the Offering Period and dividing the result by the
closing price (as defined below) on the Offering Commencement Date of such Plan
Period.

      Notwithstanding the above, no employee may be granted an Option (as
defined in Section 9) which permits his rights to purchase Common Stock under
this Plan and any other employee stock purchase plan (as defined in Section
423(b) of the Code) of the Company and its subsidiaries, to accrue at a rate
which exceeds $25,000 of the fair market value of such Common Stock (determined
at the Offering Commencement Date of the Plan Period) for each calendar year in
which the Option is outstanding at any time.

      The purchase price for each share purchased will be 85% of the closing
price of the Common Stock on (i) the first business day of such Plan Period or
(ii) the Exercise Date, whichever closing price shall be less. Such closing
price shall be (a) the closing price on any national securities exchange on
which the Common Stock is listed, (b) the closing price of the Common Stock on
the Nasdaq National Market or (c) the average of the closing bid and asked
prices in the over-the-counter-market, whichever is applicable, as published in
The Wall Street Journal; provided that, with respect to the first Plan Period,
if the first day of such Plan Period is the IPO Date, the closing price of the
Common Stock on the first business day of such Plan Period shall be deemed to be
the initial public offering price for the Common Stock, as set forth in the
final prospectus relating to the IPO. If no sales of Common Stock were made on
such a day, the price of the Common Stock for purposes of clauses (a) and (b)
above shall be the reported price for the next preceding day on which sales were
made.

      Each employee who continues to be a participant in the Plan on the
Exercise Date shall be deemed to have exercised his Option at the Option Price
on such date and shall be deemed to have purchased from the Company the number
of full shares of Common Stock reserved for the purpose of the Plan that his
accumulated payroll deductions on such date will pay for, but not in excess of
the maximum number determined in the manner set forth above.

      Any balance remaining in an employee's payroll deduction account at the
end of a Plan Period will be automatically refunded to the employee, except that
any balance which is less than the purchase price of one share of Common Stock
will be carried forward into the employee's payroll deduction account for the
following Offering, unless the employee elects not to participate in the
following Offering under the Plan, in which case the balance in the employee's
account shall be refunded.

      10. Issuance of Certificates. Certificates representing shares of Common
Stock purchased under the Plan may be issued only in the name of the employee,
in the name of the employee and another person of legal age as joint tenants
with rights of survivorship, or (in the

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Company's sole discretion) in the name of a brokerage firm, bank or other
nominee holder designated by the employee. The Company may, in its sole
discretion and in compliance with applicable laws, authorize the use of book
entry registration of shares in lieu of issuing stock certificates.

      11. Rights on Retirement, Death or Termination of Employment. In the event
of a participating employee's termination of employment prior to the last
business day of a Plan Period, no payroll deduction shall be taken from any pay
due and owing to an employee and the balance in the employee's account shall be
paid to the employee or, in the event of the employee's death, (a) to a
beneficiary previously designated in a revocable notice signed by the employee
(with any spousal consent required under state law) or (b) in the absence of
such a designated beneficiary, to the executor or administrator of the
employee's estate or (c) if no such executor or administrator has been appointed
to the knowledge of the Company, to such other person(s) as the Company may, in
its discretion, designate. If, prior to the last business day of the Plan
Period, the Designated Subsidiary by which an employee is employed shall cease
to be a subsidiary of the Company, or if the employee is transferred to a
subsidiary of the Company that is not a Designated Subsidiary, the employee
shall be deemed to have terminated employment for the purposes of this Plan.

      12. Optionees Not Stockholders. Neither the granting of an Option to an
employee nor the deductions from his pay shall constitute such employee a
stockholder of the shares of Common Stock covered by an Option under this Plan
until such shares have been purchased by and issued to him.

      13. Rights Not Transferable. Rights under this Plan are not transferable
by a participating employee other than by will or the laws of descent and
distribution, and are exercisable during the employee's lifetime only by the
employee.

      14. Application of Funds. All funds received or held by the Company under
this Plan may be combined with other corporate funds and may be used for any
corporate purpose.

      15. Adjustment in Case of Changes Affecting Common Stock. In the event of
a subdivision of outstanding shares of Common Stock, or the payment of a
dividend in Common Stock, the number of shares approved for this Plan, and the
share limitation set forth in Section 9, shall be increased proportionately, and
such other adjustment shall be made as may be deemed equitable by the Board or
the Committee. In the event of any other change affecting the Common Stock, such
adjustment shall be made as may be deemed equitable by the Board or the
Committee to give proper effect to such event.

      16. Merger. If the Company shall at any time merge or consolidate with
another corporation and the holders of the capital stock of the Company
immediately prior to such merger or consolidation continue to hold at least a
majority by voting power of the capital stock of the surviving corporation
("Continuity of Control"), the holder of each Option then outstanding will
thereafter be entitled to receive at the next Exercise Date upon the exercise of
such Option for each share as to which such Option shall be exercised the
securities or property which a holder of one share of the Common Stock was
entitled to upon and at the time of such merger or consolidation, and the Board
or the Committee shall take such steps in connection with

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such merger or consolidation as the Board or the Committee shall deem necessary
to assure that the provisions of Section 15 shall thereafter be applicable, as
nearly as reasonably may be, in relation to the said securities or property as
to which such holder of such Option might thereafter be entitled to receive
thereunder.

      In the event of a merger or consolidation of the Company with or into
another corporation which does not involve Continuity of Control, or of a sale
of all or substantially all of the assets of the Company while unexercised
Options remain outstanding under the Plan, (a) subject to the provisions of
clauses (b) and (c), after the effective date of such transaction, each holder
of an outstanding Option shall be entitled, upon exercise of such Option, to
receive in lieu of shares of Common Stock, shares of such stock or other
securities as the holders of shares of Common Stock received pursuant to the
terms of such transaction; or (b) all outstanding Options may be cancelled by
the Board or the Committee as of a date prior to the effective date of any such
transaction and all payroll deductions shall be paid out to the participating
employees; or (c) all outstanding Options may be cancelled by the Board or the
Committee as of the effective date of any such transaction, provided that notice
of such cancellation shall be given to each holder of an Option, and each holder
of an Option shall have the right to exercise such Option in full based on
payroll deductions then credited to his account as of a date determined by the
Board or the Committee, which date shall not be less than ten (10) days
preceding the effective date of such transaction.

      17. Amendment of the Plan. The Board may at any time, and from time to
time, amend this Plan in any respect, except that (a) if the approval of any
such amendment by the shareholders of the Company is required by Section 423 of
the Code, such amendment shall not be effected without such approval, and (b) in
no event may any amendment be made which would cause the Plan to fail to comply
with Section 423 of the Code.

      18. Insufficient Shares. In the event that the total number of shares of
Common Stock specified in elections to be purchased under any Offering plus the
number of shares purchased under previous Offerings under this Plan exceeds the
maximum number of shares issuable under this Plan, the Board or the Committee
will allot the shares then available on a pro rata basis.

      19. Termination of the Plan. This Plan may be terminated at any time by
the Board. Upon termination of this Plan all amounts in the accounts of
participating employees shall be promptly refunded.

      20. Governmental Regulations. The Company's obligation to sell and deliver
Common Stock under this Plan is subject to listing on a national stock exchange
or quotation on the Nasdaq National Market (to the extent the Common Stock is
then so listed or quoted) and the approval of all governmental authorities
required in connection with the authorization, issuance or sale of such stock.

      21. Governing Law. The Plan shall be governed by Delaware law except to
the extent that such law is preempted by federal law.


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      22. Issuance of Shares. Shares may be issued upon exercise of an Option
from authorized but unissued Common Stock, from shares held in the treasury of
the Company, or from any other proper source.

      23. Notification upon Sale of Shares. Each employee agrees, by entering
the Plan, to promptly give the Company notice of any disposition of shares
purchased under the Plan where such disposition occurs within two (2) years
after the date of grant of the Option pursuant to which such shares were
purchased.

      24. Special Provisions for First Plan Period. If the first day of the
first Plan Period is the IPO Date, the following provisions of this Section 24
shall apply with respect to the first Plan Period notwithstanding any provision
of the Plan to the contrary:

            (a) Every eligible employee shall automatically become a participant
in the Plan for the first Plan Period at the highest percentage of Compensation
permitted under Section 5. No payroll deductions shall be required for the first
Plan Period; however, a participant may, at any time after the effectiveness of
the Plan's Registration Statement on Form S-8, elect to have payroll deductions
up to the aggregate amount which would have been credited to his or her account
if a deduction of fifteen percent (15%) of the Compensation which he or she
received on each pay day during the first Plan Period had been made (the
"Maximum Amount") or decline to participate by filing an appropriate
subscription agreement.

            (b) Upon the automatic exercise of a participant's option on the
Exercise Date for the first Plan Period, a participant shall be permitted to
purchase shares with (i) the accumulated payroll deductions in his or her
account, if any, (ii) a direct payment from the participant, or (iii) a
combination thereof; provided, however that the total amount applied to the
purchase may not exceed the Maximum Amount.

      25. Withholding. Each employee shall, no later than the date of the event
creating the tax liability, make provision satisfactory to the Board for payment
of any taxes required by law to be withheld in connection with any transaction
related to Options granted to or shares acquired by such employee pursuant to
the Plan. The Company may, to the extent permitted by law, deduct any such taxes
from any payment of any kind otherwise due to an employee.

      26. Effective Date and Approval of Shareholders. The Plan shall take
effect on the IPO Date, subject to approval by the shareholders of the Company
as required by Section 423 of the Code, which approval must occur within twelve
months of the adoption of the Plan by the Board.


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