<PAGE>

                                                                   EXHIBIT 10.44

                             BROOKS AUTOMATION, INC.

                       NONQUALIFIED STOCK OPTION AGREEMENT

      Nonqualified Stock Option Agreement (the "Option") made effective as of
the <<OPTION_DATE>>, between Brooks Automation, Inc. (the "Corporation"), and
<<FIRST_NAME>> <<MIDDLE_NAME>> <<LAST_NAME>> (the "Recipient"), an employee of
the Corporation, a Parent or a Subsidiary, pursuant to the Brooks Automation,
Inc. 2000 Equity Incentive Plan, as it may be amended from time to time (the
"2000 Plan").

                              W I T N E S S E T H:

      WHEREAS, on February 24, 2000, the Corporation adopted the 2000 Plan which
provides for the issuance of stock options, and

      WHEREAS, the Corporation and the Recipient desire to enter into an
agreement whereby the Corporation will grant the Recipient an option to purchase
shares of the Common Stock, $.01 par value, of the Corporation (the "Stock"),
and this option is intended to qualify as a Nonqualified Stock Option;

      NOW, THEREFORE, for good and valuation consideration, the receipt and
sufficiency of which is hereby acknowledged, the Corporation and the Recipient
agrees as follows:

      1. Grant of Option.

      Pursuant to the terms and conditions of the 2000 Plan and this Option, the
Corporation hereby grants to the Recipient an Option to purchase, as provided in
Section 3 hereof, all or any part of a total of <<SHARES_GRANTED>> shares of
Stock (the "Option Shares"). This Option is expressly subject to all of the
terms and conditions contained in this Option or in the 2000 Plan, which is
hereby incorporated herein by reference. All capitalized terms not defined in
this Option have the meanings specified in the 2000 Plan.

      2. Purchase Price.

      The price at which the Option Shares may be purchased shall be
<<OPTION_PRICE>> per share (the "Option Exercise Price"). This price is not less
than the Fair Market Value of the Stock on the date of this Option.

      3. Vesting and Exercise of Option.

Subject to the provisions of Section 4 and the right of the Corporation to
accelerate the date upon which any or all of the shares covered by this Option
becomes exercisable, the Recipient shall become entitled to purchase the
indicated percentage of the Option Shares as follows:

                                      - 1 -
<PAGE>

<TABLE>
<CAPTION>
Period of Time Elapsed From Date of Option                     Percentage of Total Shares Vesting
------------------------------------------                     ----------------------------------
<S>                                                            <C>
       One year                                                                25%

       Each 3 month period thereafter for the next 36 months            Additional 6.25%
</TABLE>

      If Recipient has attained age 55 and completed at least five years of
continuous employment with the Corporation on the date of termination of
employment with the Corporation, other than termination due to death, Permanent
Disability or termination for cause (a "Retirement"), then the Option Shares
shall continue to vest in accordance with the original vesting schedule without
regard to the continuous employment requirement.

Notwithstanding any provision herein to the contrary, in no event may this
Option be exercised after seven years from the date of this Option (the
"Expiration Date").

      4. Termination of Relationship.

If the Recipient ceases to be employed by the Corporation (a "Termination"),
then this Option may be exercised as to all vested Option Shares with respect to
which Recipient could exercise this Option on the date of Termination, and which
shares have not been previously purchased, until the earlier of Expiration Date,
or:

            (i) in the case of termination by reason of death or Permanent
            Disability, one year after termination of employment;

            (ii) in the case of any other termination, other than termination
            for cause, three months after the termination of employment; or

            (iii) in the case of a Retirement, the full life of the Option
            without regard to any requirement that the retiree continue his or
            her employment with the Corporation.

Notwithstanding any provision herein to the contrary the foregoing, in the case
of termination for cause (as defined in the governing employment agreement, if
any, or as determined in the Corporation's sole discretion), the ability to
exercise this Option may be terminated on such earlier date as the Corporation
may specify, and such date may be set so as to prevent the Recipient from
further exercising any portion of this Option.

      5. Nontransferability; Persons Able to Exercise.

      The Option may not be transferred other than by will or the laws of
descent and distribution. During the life of the Recipient, only the Recipient
may exercise this Option. If the Recipient dies while still affiliated with the
Corporation, or during the periods specified in Section 4, this Option may be
exercised by his executors, administrators, legatees or distributees,

                                     - 2 -
<PAGE>

provided that such person or persons comply with the provisions of this Option
applicable to the Recipient.

      6. Method of Exercising Option.

      The Option may be exercised, in whole or in part, by written notice to the
Corporation. The written notice specified in this Section must be accompanied by
payment of the Option Exercise Price for the shares being purchased. Payment
shall be made in cash, unless the Corporation, in its sole discretion,
authorizes payment to be made in shares of the Corporation or a combination of
such shares and cash. As soon as practical after receipt of this notice and
payment, the Corporation shall deliver a certificate or certificates
representing the purchased shares registered in the name of the person or
persons exercising this Option. In the event this Option is exercised by any
person other than the Recipient, the notice shall be accompanied by appropriate
proof of the right of such person to exercise this Option. All shares purchased
upon the exercise of this Option and payment of the full Option Exercise Price
will be fully paid and nonassessable.

      7. Stock Adjustments.

      If there shall be any change in the Stock through merger, consolidation,
reorganization, recapitalization, or other change in the corporate structure of
the Corporation, appropriate adjustments in the total number and kind of shares
subject to this Option shall be made by the Corporation as provided in the 2000
Plan.

      8. No Rights Other Than Those Expressly Created.

      Neither this Option nor any action taken hereunder shall be construed as
(i) giving the Recipient any right to be retained in the employ of, or continue
to be affiliated with, the Corporation, (ii) giving the Recipient any equity or
interest of any kind in any assets of the Corporation, or (iii) creating a trust
of any kind or a fiduciary relationship of any kind between the Recipient and
the Corporation. As to any claim for any unpaid amounts under this Option, any
person having a claim for payments shall be unsecured creditor. The Recipient
shall not have any of the rights of a stockholder with respect to any Option
Shares until such time as this Option has been exercised and Option Shares have
been issued.

      9. Compliance with Laws.

            (a) Withholding of Taxes. Pursuant to applicable federal, state,
local or foreign laws, the Corporation may be required to collect or withhold
income or other taxes from Recipient upon the grant of this Option, the exercise
of this Option, or at some other time. The Corporation may require, as a
condition to the exercise of this Option, or demand, at such other time as it
may consider appropriate, that the Recipient pay the Corporation the amount of
any taxes which the Corporation may determine is required to be collected or
withheld, and the Recipient shall comply with the requirement or demand of the
Corporation.

            (b) Securities Law Compliance. Upon exercise (or partial exercise)
of this Option, the Recipient shall make such representations and furnish such
information as may, in the opinion of counsel for the Corporation, be
appropriate to permit the Corporation to issue or transfer the Option Shares in
compliance with the provisions of applicable federal or state

                                     - 3 -
<PAGE>

securities laws. The Corporation, in its discretion, may postpone the issuance
and delivery of Option Shares upon any exercise of this Option until completion
of such registration or other qualification of such shares under any federal or
state laws, or stock exchange listing, as the Corporation may consider
appropriate. The Corporation may require that prior to the issuance or transfer
of Option Shares upon exercise of this Option, the Recipient enter into a
written agreement to comply with any restrictions on subsequent disposition that
the Corporation deems necessary or advisable under any applicable federal and
state securities laws. Certificates of Stock issued hereunder may bear a legend
to reflect such restrictions.

            (c) General. No Option Shares shall be issued upon exercise of this
Option unless and until the Corporation is satisfied, in its sole discretion,
that there has been compliance with all legal requirements applicable to the
issuance of such Option Shares.

      10. Miscellaneous.

            (a) Provisions of the Plan. The Option hereby granted is expressly
subject to all of the terms and conditions contained in this Option and in the
2000 Plan, except those which are expressly applicable only to "2000 Plan ISOs",
and the 2000 Plan is hereby incorporated herein by reference. All capitalized
terms not defined in this Option have the meanings specified in the 2000 Plan.
This stock option is not intended to be an Incentive Stock Option, as that term
is described in Section 422 of the Internal Revenue Code of 1986, as amended.

            (b) Discretion of the Committee. Unless otherwise explicitly
provided, the Committee, as defined in the Plan, shall make all determinations
required to be made hereunder, including determinations required to be made by
the Corporation, and shall interpret all provisions of this Option, as it deems
necessary or desirable, in its sole and unfettered discretion. Such
determinations and interpretations shall be binding and conclusive to the
Corporation and the Recipient. The Committee, in its sole discretion, is
authorized to accelerate the time at which this Option may be exercised.

            (c) Reservation of Shares. During the term of this Option, the
Corporation shall at all times reserve and keep available shares of Stock
sufficient to satisfy the requirements of this Option.

            (d) Amendment. This Option may only be modified or amended by a
writing signed by both parties.

            (e) Notices. Any notices required to be given under this Option
shall be sufficient if in writing and if hand-delivered or if sent by first
class mail and addressed as follows:

IF TO THE CORPORATION:

Brooks Automation, Inc.
15 Elizabeth Drive
Chelmsford, MA  01824

                                     - 4 -
<PAGE>

IF TO THE RECIPIENT:

<<FIRST_NAME>> <<MIDDLE_NAME>> <<LAST_NAME>>
<<ADDRESS_LINE_1>> <<ADDRESS_LINE_2>> <<ADDRESS_LINE_3>>
<<CITY>>, <<STATE>> <<ZIP_CODE>> <<COUNTRY>>

or to such other address as either party may designate under the provisions
hereof.

            (f) Successors and Assigns. The rights and obligations of the
Corporation under this Option shall inure to the benefit of and be binding upon
the successors and assigns of the Corporation.

            (g) Applicable Law. All rights and obligations under this Option
shall be governed by the laws of the Commonwealth of Massachusetts.

            (h) Paragraph Headings. The paragraph headings used in this Option
are for convenience of reference only, and are not to be construed as part of
this Option.

      IN WITNESS WHEREOF, the parties have executed this Option as an instrument
under seal effective as of the date written on the first page of this Option.

BROOKS AUTOMATION, INC.

      By: /s/ Lynda M. Avallone
          -------------------------
          Lynda M. Avallone
          Vice President and Corporate Treasurer

Recipient:

__________________________________

<<FIRST_NAME>> <<MIDDLE_NAME>> <<LAST_NAME>>

                                     - 5 -