Document:

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                                                                     Exhibit 4.1
NEI-
                                    [LOGO]

                             NETWORK ENGINES, INC.

             INCORPORATED UNDER THE LAWS OF THE STATE OF DELAWARE

                                 COMMON STOCK

THIS CERTIFICATE IS TRANSFERABLE                             CUSIP 64121A 10 7
IN BOSTON, MA OR NEW YORK, NY                                SEE REVERSE FOR
                                                             CERTAIN DEFINITIONS

THIS CERTIFIES THAT _________________________________________________________

is the owner of _____________________________________________________________

FULLY PAID AND NON-ASSESSABLE SHARES OF COMMON STOCK OF THE PAR VALUE OF ONE
CENT ($.01) EACH OF

                             NETWORK ENGINES, INC.

(hereinafter called the "Corporation") transferable upon the books of the
Corporation by the holder hereof in person or by duly authorized attorney upon
surrender of this Certificate properly endorsed.  This Certificate and the
shares represented hereby are issued and shall be subject to all the provisions
of the Second Amended and Restated Certificate of Incorporation and Second
Amended and Restated By-Laws of the Corporation as from time to time amended
(copied of which are on file with the Corporation) to all of which the holder,
by acceptance hereof, assents.  This Certificate is not valid unless
countersigned and registered by the Transfer Agent and Registrar.

     IN WITNESS WHEREOF, the Corporation has caused this Certificate to be
signed by the facsimile signatures of its duly authorized officers and its
facsimile corporate seal to be hereunto affixed.

Dated:__________                   COUNTERSIGNED AND REGISTERED:
                                   EQUISERVE TRUST COMPANY, N.A.
                                   TRANSFER AGENT AND REGISTRAR

                                   BY_______________________________
                                          AUTHORIZED SIGNATURE

/s/ Douglas G. Bryant              /s/ Lawrence Genovesi
VICE PRESIDENT, SECRETARY          CHAIRMAN, PRESIDENT AND
AND TREASURER                      CHIEF EXECUTIVE OFFICER

                               [CORPORATE SEAL]
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                             NETWORK ENGINES, INC.

     The Corporation is authorized to issue more than one class of stock.
A statement of the powers, designations, preferences, and the relative
participating, optional, or other rights of each class and series of stock and
the qualifications, limitations or restrictions thereon will be provided without
charge to each stockholder upon request to the Corporation.

     The following abbreviations, when used in the inscription on the face of
this Certificate, shall be construed as though they were written out in full
according to applicable laws or regulations:

<TABLE>
<CAPTION>
TEN COM    - as tenants in common          UNIF GIFT MIN ACT - ______Custodian_______
TEN ENT    - as tenants by the entireties                      (Cust)         (Minor)
JT TEN     - as joint tenants with right                       under Uniform Gifts to Minors
             of survivorship and not as                        Act________________
             tenants in common                                        (State)
<S> <C>
</TABLE>

    Additional abbreviations may also be used though not in the above list.

For value received, _____________________ hereby sell, assign and transfer unto

PLEASE INSERT SOCIAL SECURITY OR OTHER
INDENTIFYING NUMBER OF ASSIGNEE

______________________________

_____________________________________________________________________________
  PLEASE PRINT OR TYPEWRITE NAME AND ADDRESS, INCLUDING ZIP CODE, OF ASSIGNEE

_____________________________________________________________________________

_____________________________________________________________________________

_____________________________________________________________________________
of the capital stock represented by the within Certificate, and do hereby
irrevocably constitute and appoint

_____________________________________________________________________________
to transfer the said stock on the books of the within-named Corporation with
full power of substitution in the premises.

Dated,__________________     ________________________________________________
                             NOTICE: The signature to this assignment must
                             correspond with the name as written upon the face
                             of the Certificate, in every particular, without
                             alteration or enlargement, or any change
                             whatsoever.

SIGNATURE(S) GUARANTEED:_____________________________________________________
                        THE SIGNATURE(S) SHOULD BE GUARANTEED BY AN ELIGIBLE
                        LOAN ASSOCIATIONS AND CREDIT UNIONS WITH MEMBERSHIP IN
                        AN APPROVED SIGNATURE GUARANTEE MEDALLION PROGRAM),
                        PURSUANT TO S.E.C. RULE 17Ad-15.

<TABLE>
<S>                                                      <C>
              AMERICAN BANK NOTE COMPANY                                PRODUCTION COORDINATOR:
                55TH and SANSOM STREET                                BELINDA BECK: 215-764-8619
                PHILADELPHIA, PA  19139                                 PROOF OF APRIL 24, 2000
                    (215) 764-8600                                       NETWORK ENGINES, INC.
                                                                              H 66191 BK
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           SALES:  DAN BURNS:  617-786-7600                                 OPERATOR:    JW
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           /HOME16/LIVE JOBS/N/NETWORK 66191                                      NEW
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</TABLE><PAGE>

                                                                   Exhibit 10.4

                             NETWORK ENGINES, INC.

                       2000 EMPLOYEE STOCK PURCHASE PLAN

     The purpose of this Plan is to provide eligible employees of Network
Engines, Inc. (the "Company") and certain of its subsidiaries with opportunities
to purchase shares of the Company's common stock, $.01 par value (the "Common
Stock").  Seven Hundred and Fifty Thousand (750,000) shares of Common Stock in
the aggregate 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, including Directors who are
        -----------
employees, 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 are employees of the Company or a Designated Subsidiary on
     the first day of the applicable Plan Period (as defined below).

     No employee may be granted an option hereunder if such employee,
immediately after the option is granted, owns five percent (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
15 and May 15, or the first business day thereafter (the "Offering Commencement
Dates"). Each Offering Commencement Date will begin a six (6) 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 first date the Company has
filed an effective registration statement on Form S-8 with the Securities and
Exchange Commission for purposes of registering

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under the Securities Act of 1933 all shares of the Common Stock issuable under
this Plan, and shall end on November 15, 2000.

     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) 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 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, 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 fifteen percent (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 up to fifteen percent (15%) in
increments of one percent (1%). The minimum payroll deduction is initially one
percent (1%) of Compensation and may be revised from time to time by the Board
or the Committee.

     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.

     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).

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     7. Interest. Interest will not be paid on any employee accounts, except to
        --------
the extent that the Board or the Committee, in its sole discretion, elects to
credit employee accounts with interest at such per annum rate as it may from
time to time determine.

     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 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.

     The purchase price for each share purchased will be eighty-five percent
(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.  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

                                      -3-
<PAGE>

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 80%
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

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<PAGE>

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 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.

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

     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. Effective Date and Approval of Shareholders. The Plan shall take effect
         -------------------------------------------
on March 16, 2000 subject to approval by the shareholders of the Company as
required by Section 423 of the Code, which approval must occur within twelve
(12) months of the adoption of the Plan by the Board.

          Adopted by the Board of Directors: March 16, 2000

          Approved by the stockholders: _____________, 2000

                                      -6-

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