<PAGE>
                                                                    EXHIBIT 10.1

        AGREEMENT dated this 31st day of July, 2002 between Nastech
Pharmaceutical Company Inc., a Delaware corporation (the "Company") with offices
at 45 Adams Avenue, Hauppauge, NY and Gregory L. Weaver (the "Executive").

                              W I T N E S S E T H :

        WHEREAS, the Company and the Executive wish to enter into a
Change-In-Control Severance Agreement on the following terms and conditions:

        (1) In the event Executive's employment with the Company is terminated
within one year following the occurrence of a Change of Control (other than as a
consequence of death or disability) either (x) by the Company for any reason
other than for Cause, or (y) by Executive for Good Reason, then Executive shall
be entitled to receive the following:

        (i) Base Salary: Executive's annual base salary as in effect at the date
of termination shall be paid on the date of termination;

        (ii) Target Incentive Compensation: The amount of the Executive's target
incentive compensation under the applicable Executive Bonus Plan for the fiscal
year in which the date of termination occurs shall be paid on the date of
termination; and

        (iii) Other Benefits: Notwithstanding the vesting period provided for in
the Company's Stock Option Plan and any related stock option agreements between
the Company and the Executive for stock options ("options") granted Executive by
the Company all of such options shall be fully vested and exercisable upon a
Change of Control and termination of employment.

        (a) For purposes of this Agreement, the term "Good Reason" shall mean a
termination of employment as a result of a substantial diminution in the
Executive's responsibilities, or base salary below $235,000 or a demotion in
title or status.

        (b) For purposes of this Agreement, the term "Cause" shall mean (i) the
Executive's willful, repeated or neglectful failure to perform his duties or to
comply with any reasonable or proper direction given by or on behalf of the
Company's Board of Directors following ten (10) days written notice to such
effect; (ii) the Executive being guilty of serious misconduct on the Company's
premises or elsewhere, whether during the performance of his duties or not,
which may cause damage to the reputation of the Company or render it difficult
for the Executive to satisfactorily continue to perform his duties; (iii) the
Executive being found guilty in a criminal court of any offense of a nature
likely to affect the reputation of the Company or to prejudice its interests if
the Executive were to continue to be employed by the Company; (iv) the
Executive's commission of any act of fraud, theft or dishonesty, or any
intentional tort against the Company; or (v) the Executive's violation of any of
the material terms, covenants, representations or warranties contained in any
Agreement between the Executive and the Company.

        (c) For purposes of this Agreement, the term "Change of Control" shall
mean:

        (i) The acquisition, other than from the Company, by any individual,
entity or group (within the meaning of Rule 13d-3 promulgated under the Exchange
Act or any successor provision) (any of the foregoing described in this
Paragraph 18.b.i hereafter a "Person") of 50% or more of either (a) the then
outstanding shares of Capital Stock of the Company (the "Outstanding Capital
Stock") or (b) the combined voting power of the then outstanding voting
securities of the Company entitled to vote generally in the


<PAGE>
election of directors (the" Voting Securities"), provided, however, that any
acquisition by (x) the Company or any of its subsidiaries, or any employee
benefit plan (or related trust) sponsored or maintained by the Company or any of
its subsidiaries or (y) any Person that is eligible, pursuant to Rule 13d-1(b)
under the Exchange Act, to file a statement on Schedule 13G with respect to its
beneficial ownership of Voting Securities, whether or not such Person shall have
filed a statement on Schedule 13G, unless such Person shall have filed a
statement on Schedule 13D with respect to beneficial ownership of 50% or more of
the Voting Securities or (z) any corporation with respect to which, following
such acquisition, more than 60% of, respectively, the then outstanding shares of
common stock of such corporation and the combined voting power of the then
outstanding voting securities of such corporation entitled to vote generally in
the election of directors is then beneficially owned, directly or indirectly, by
all or substantially all of the individuals and entities who were the beneficial
owners, respectively, of the Outstanding Capital Stock and Voting Securities
immediately prior to such acquisition in substantially the same proportion as
their ownership, immediately prior to such acquisition, of the Outstanding
Capital Stock and Voting Securities, as the case may be, shall not constitute a
Change of Control; or

        (ii) Individuals who, as of the Effective Date, constitute the Board
(the "Incumbent Board") cease for any reason to constitute at least a majority
of the Board, provided that any individual becoming a director subsequent to the
date hereof whose election or nomination for election by the Company's
shareholders, was approved by a vote of at least a majority of the directors
then comprising the Incumbent Board shall be considered as though such
individual were a member of the Incumbent Board, but excluding, for this
purpose, any such individual whose initial assumption of office is in connection
with an actual or threatened election contest relating to the election of the
Directors of the Company (as such terms are used in Rule 14a-11 of Regulation
14A, or any successor section, promulgated under the Exchange Act); or

        (iii) Approval by the shareholders of the Company of a reorganization,
merger or consolidation (a "Business Combination"), in each case, with respect
to which all or substantially all holders of the Outstanding Capital Stock and
Voting Securities immediately prior to such Business Combination do not,
following such Business Combination, beneficially own, directly or indirectly,
more than 60% of, respectively, the then outstanding shares of common stock and
the combined voting power of the then outstanding voting securities entitled to
vote generally in the election of directors, as the case may be, of the
corporation resulting from the Business Combination; or

        (iv) (a) a complete liquidation or dissolution of the Company or (b) a
sale or other disposition of all or substantially all of the assets of the
Company other than to a corporation with respect to which, following such sale
or disposition, more than 60% of, respectively, the then outstanding shares of
common stock and the combined voting power of the then outstanding voting
securities entitled to vote generally in the election of directors is then owned
beneficially, directly or indirectly, by all or substantially all of the
individuals and entities who were the beneficial owners, respectively, of the
Outstanding Capital Stock and Voting Securities immediately prior to such sale
or disposition in substantially the same proportion as their ownership of the
Outstanding Capital Stock and Voting Securities, as the case may be, immediately
prior to such sale or disposition.

        2. Entire Agreement; Waiver. This Agreement contains the entire
understanding of the parties and may not be changed orally but only by an
agreement in writing, signed by the party against whom enforcement of any
waiver, change, modification or discharge is sought. Waiver of or failure to
exercise any rights provided by this Agreement in any respect shall not be
deemed a waiver of any further or future rights.

        3. Binding Effect; Assignment. The rights and obligations of this
Agreement shall bind and inure to the benefit of any successor of the Company by
reorganization, merger or consolidation, or any assignee of


<PAGE>
all or substantially all of the Company's business or properties. The
Executive's rights hereunder are personal to and shall not be transferable or
assignable by the Executive.

        4. Headings. The headings contained in this Agreement are for reference
purposes only and shall not affect the meaning or interpretation of this
Agreement.

        5. Governing Law; Arbitration. This Agreement shall be construed in
accordance with and governed for all purposes by the laws and public policy of
the State of New York applicable to contracts executed and to be wholly
performed within such state. Any dispute or controversy arising out of or
relating to this Agreement shall be settled by arbitration in accordance with
the rules of the American Arbitration Association and judgment upon the award
may be entered in any court having jurisdiction thereover. The arbitration shall
be held in Seattle, Washington or in such other place as the parties hereto may
agree.

        6. Severability. The parties agree that if any one or more of the terms,
provisions, covenants or restrictions of this Agreement shall be determined by a
court of competent jurisdiction to be invalid, void or unenforceable, the
remainder of the terms, provisions, covenants and restrictions of this Agreement
shall remain in full force and effect and shall in no way be affected, impaired
or invalidated.

        7. Counterparts. This Agreement maybe executed in several counterparts,
each of which shall be deemed to be an original, but all of which together will
constitute one and the same Agreement.

   IN WITNESS WHEREOF, NASTECH PHARMACEUTICAL COMPANY INC. has caused this
instrument to be signed by a duly authorized officer and the Executive has
hereunto set his hand the day and year first above written.

NASTECH PHARMACEUTICAL COMPANY INC.

By: /s/ Steven C. Quay, M.D., Ph.D.
    -------------------------------


    /s/ Gregory L. Weaver
    -----------------------
    GREGORY L. WEAVER