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Exhibit 10.2

AMENDED AND RESTATED EMPLOYMENT AGREEMENT

    THIS AMENDED AND RESTATED EMPLOYMENT AGREEMENT (this "Agreement"), effective
as of June 3, 2001, is made by and between NANOGEN, INC., a Delaware corporation
(hereinafter the "Company"), and HOWARD C. BIRNDORF, (hereinafter "Executive").

RECITALS

    WHEREAS, the Company and Executive entered into an Employment Agreement,
dated as of October 29, 1999, as amended by the First Amendment to Employment
Agreement, dated as of July 28, 2000 (collectively, the "Previous Employment
Agreements");

    WHEREAS, the Company and Executive wish to amend and restate the Previous
Employment Agreements.

    NOW, THEREFORE, the Company and Executive, in consideration of the
Executive's continued employment with the Company, agree as follows:

ARTICLE I.

TERM OF AGREEMENT

    A.  Commencement Date.  The terms of this Agreement shall govern Executive's
employment with the Company from June 3, 2001 and this Agreement shall expire on
October 29, 2002, which is a period of three (3) years from October 29, 1999,
the original commencement date of the October 29, 1999 Employment Agreement
between Executive and the Company, unless terminated earlier pursuant to
Article 6.

    B.  Renewal.  The term of this Agreement shall be automatically renewed for
successive, additional three (3) year terms unless either party delivers written
notice to the other at least ninety (90) days prior to the expiration date of
this Agreement of an intention to terminate this Agreement or to renew it for a
term of less than three (3) years but not less than (1) year. If the term of
this Agreement is renewed for a term of less than three (3) years, then
thereafter the term of this Agreement shall be automatically renewed for
successive, additional identical terms unless either party delivers a written
notice to the other at least ninety (90) days prior to a termination date of
this Agreement of an intention to terminate this Agreement or to renew it for a
different term of not less than one (1) year. Any renewal bonus will be
negotiated as mutually agreed to at the time of any renewal of this Agreement.

    If this Agreement is not renewed at the end of any term hereof by the
Company for any reason except death, disability or retirement of Executive,
notwithstanding anything herein elsewhere contained, Executive shall be paid his
salary, as provided for in Section 3.A hereof, and receive the other benefits
applicable under Article 4 hereof, for an additional eighteen (18) months after
the termination date hereof.

ARTICLE II.

EMPLOYMENT DUTIES

    A.  Title/Responsibilities.  Executive hereby accepts employment with the
Company pursuant to the terms and conditions hereof. Executive agrees to serve
the Company in the position of Executive Chairman and Chairman of the Board.
Executive shall report to the Board of Directors of the Company (the "Board").
Executive shall have the powers and duties commensurate with such position,

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including but not limited to, hiring personnel necessary (in the judgment of the
Board) to carry out the responsibilities for such position.

    B.  Full Time Attention.  Executive shall devote his best efforts and his
full business time and attention to the performance of the services customarily
incident to such office and to such other services as the Board may reasonably
request, provided that Executive may (i) continue to serve as a member of the
Board of Directors of Graviton, Inc., provided that such service does not
interfere with Executive's ability to render services hereunder, and (ii) may
also serve on the Boards of Directors of a limited number of other companies
with the prior written consent of the Board.

    C.  Other Activities.  Except upon the prior written consent of the Board of
Directors, Executive shall not during the period of employment engage, directly
or indirectly, in any other business activity (whether or not pursued for
pecuniary advantage) that is or may be competitive with, or that might place him
in a competing position to that of the Company or any other corporation or
entity that directly or indirectly controls, is controlled by, or is under
common control with the Company (an "Affiliated Company"), provided that
Executive may own less than two percent of the outstanding securities of any
such publicly traded competing corporation.

    D.  Directorships.  Executive will be nominated for reelection to the
Company's Board of Directors if the By-Laws so require it. At the pleasure of
the Company's stockholders. Executive agrees to serve as a Director on the
Company's Board of Directors at no additional compensation.

ARTICLE III.

COMPENSATION

    A.  Base Salary.  Executive shall receive a Base Salary at an annual rate of
three hundred sixty-five thousand dollars ($365,000), payable in accordance with
the Company's customary payroll practices. The Company's Board of Directors
shall provide Executive with annual performance reviews, and, thereafter,
Executive shall be entitled to such Base Salary as the Board of Directors may
from time to time establish in its sole discretion.

    B.  Incentive Bonuses.  Executive shall receive a Basic Bonus of one hundred
thousand dollars ($100,000) per year, payable in equal installments not less
often than quarterly.

    C.  Achievement Bonus.  The Company shall pay Executive an Achievement Bonus
of up to 60% of Executive's Base Salary annually based upon achievement by the
Company of its corporate goals as established and determined by the Board of
Directors annually and for other achievements by the Company or the Executive
during the year as approved by the Compensation Committee. The Board of
Directors or Compensation Committee, as applicable, shall, in their respective
sole discretion, determine whether such corporate or other goals have been
attained or other achievements have occurred.

    D.  Transaction Bonus.  In addition, in the event of a transaction involving
a Change in Control approved by the Company's Board of Directors, which
transaction results in the receipt by the Company's stockholders of
consideration with a value representing, in the sole judgment of the Board of
Directors, a significant premium over the average of the closing prices per
share of the Company's common stock as quoted on the Nasdaq National Market for
20 trading days ending one day prior to the public announcement of such
transaction (a "Change in Control Transaction"), Executive shall be paid a
Transaction Bonus at the closing of such a transaction in the amount equal to
three (3) times 60% of Executive's Base Salary in effect immediately preceding
the closing of such a transaction. Executive shall also be paid said Transaction
Bonus if the Company enters into a transaction approved by the Board of
Directors which is not a Change in Control Transaction, but which, nonetheless,
involves a significant change in the ownership of the Company or the composition
of the Board of Directors of the Company, and which results in significant
additional value for the Company's

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stockholders, as determined by the Board of Directors in its sole discretion and
as specifically designated a significant event by the Board of Directors (a
"Significant Event"). In the event Executive receives a Transaction Bonus, no
Achievement Bonus will be paid to Executive in the year in which such
Transaction Bonus is paid.

    If the Company enters into a transaction which is a Change in Control
Transaction, then all of the Executive's stock options received before the
effective date of the transaction shall become exercisable in full and all of
the shares of the common stock of the Company awarded to Executive under the
Company's 1997 Stock Incentive Plan and the 1993 Stock Option/Stock Issuance
Plan received before the effective date of the transaction shall become fully
vested. If the Company enters into a transaction which is not a Change in
Control Transaction but which is a Significant Event, then the Board of
Directors may, in its sole discretion, determine that all, or a portion, of the
Executive's stock options received before the effective date of the transaction
shall become exercisable in full and all, or a portion, of the shares of the
common stock of the Company awarded to Executive under the Company's 1997 Stock
Incentive Plan and the 1993 Stock Option/Stock Issuance Plan received before the
effective date of the transaction shall become fully vested.

    E.  Withholdings.  All compensation and benefits to Executive hereunder
shall be subject to all federal, state, local and other withholdings and similar
taxes and payments required by applicable law.

ARTICLE IV.

EXPENSE ALLOWANCES AND FRINGE BENEFITS

    A.  Vacation.  Executive shall be entitled to three (3) weeks, plus one
(1) additional day for each completed year of employment with the Company, of
annual paid vacation during the term of this Agreement.

    B.  Benefits.  During the term of this Agreement, the Company shall also
provide Executive with the usual health insurance benefits it generally provides
to its other senior management employees, other than life insurance (which shall
be paid directly by Executive). As Executive becomes eligible in accordance with
criteria to be adopted by the Company, the Company shall provide Executive with
the right to participate in and to receive benefits from accident, disability,
medical, pension, bonus, stock, profit-sharing and savings plans and similar
benefits made available generally to employees of the Company as such plans and
benefits may be adopted by the Company, provided that Executive shall during the
term of this Agreement be entitled to receive at a minimum standard medical and
dental benefits similar to those typically afforded to Chief Executive Officers
in similar sized biotechnology companies, excluding life insurance. The amount
and extent of benefits to which Executive is entitled shall be governed by the
specific benefit plan as it may be amended from time to time.

    C.  Company Loans.  Upon the closing of a transaction approved by the
Company's Board of Directors involving a Change of Control or a Significant
Event, all amounts outstanding with respect to the Loans made by Company to
Executive and listed on Schedule A hereto, shall be forgiven on a pro rata basis
over a four (4) year period commencing on the Executive's original date of
employment by the Company (including any accrued and unpaid interest).

    D.  Business Expense Reimbursement.  During the term of this Agreement,
Executive shall be entitled to receive proper reimbursement for all reasonable
out-of-pocket expenses incurred by him (in accordance with the policies and
procedures established by the Company for its senior executive officers) in
performing services hereunder, provided Executive properly accounts therefor.

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ARTICLE V.

CONFIDENTIALITY

    A.  Proprietary Information.  Executive represents and warrants that he has
executed and delivered to the Company the Company's standard Proprietary
Information, Inventions and Dispute Resolution Agreement in form acceptable to
the Company's counsel.

    B.  Return of Property.  All documents, records, apparatus, equipment and
other physical property which is furnished to or obtained by Executive in the
course of his employment with the Company shall be and remain the sole property
of the Company. Executive agrees that, upon the termination of his employment,
he shall return all such property (whether or not it pertains to Proprietary
Information as defined in the Proprietary Information, Inventions and Dispute
Resolution Agreement), and agrees not to make or retain copies, reproductions or
summaries of any such property.

ARTICLE VI.

TERMINATION

    A.  By Death.  The period of employment shall terminate automatically upon
the death of Executive. In such event, the Company shall pay to Executive's
beneficiaries or his estate, as the case may be, any accrued Base Salary, any
bonus compensation to the extent earned, any vested deferred compensation (other
than pension plan or profit-sharing plan benefits which will be paid in
accordance with the applicable plan), any benefits under any plans of the
Company in which Executive is a participant to the full extent of Executive's
rights under such plans, any accrued vacation pay and any appropriate business
expenses incurred by Executive in connection with his duties hereunder, all to
the date of termination (collectively "Accrued Compensation"), but no other
compensation or reimbursement of any kind, including, without limitation,
severance compensation, and thereafter, the Company's obligations hereunder
shall terminate.

    B.  By Disability.  If Executive is prevented from properly performing his
duties hereunder by reason of any physical or mental incapacity for a period of
more than 90 days in the aggregate in any 365-day period, then, to the extent
permitted by law, the Company may terminate the employment on the 90th day of
such incapacity. In such event, the Company shall pay to Executive all Accrued
Compensation, and shall continue to pay to Executive the Base Salary until such
time (but not more than 90 days following termination), as Executive shall
become entitled to receive disability insurance payments under the disability
insurance policy maintained by the Company, which disability policy shall
provide for full payment of Executive's Base Salary during the period of
disability, but no other compensation or reimbursement of any kind, including
without limitation, severance compensation, and thereafter the Company's
obligations hereunder shall terminate. Nothing in this Section shall affect
Executive's rights under any disability plan in which he is a participant.

    C.  By Company for Cause.  The Company may terminate Executive's employment
for Cause (as defined below) without liability at any time with or without
advance notice to Executive. The Company shall pay Executive all Accrued
Compensation, but no other compensation or reimbursement of any kind, including
without limitation, severance compensation, and thereafter the Company's
obligations hereunder shall terminate. Termination shall be for "Cause" in the
event of the occurrence of any of the following: (a) any intentional action or
intentional failure to act by Executive which was performed in bad faith and to
the material detriment of the Company; (b) Executive intentionally refuses or
intentionally fails to act in accordance with any lawful and proper direction or
order of the Board; (c) gross negligence by Executive in carrying out the duties
of employment; or (d) Executive is convicted of a felony crime involving moral
turpitude, provided that in the event that any of the foregoing events is
capable of being cured, the Company shall provide written notice to Executive
describing the nature of such event and Executive shall thereafter have five
(5) business days to cure such event.

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    D.  At Will.  At any time, the Company may terminate Executive's employment
without liability other than as set forth below, for any reason not specified in
Section 6.C above, by giving thirty (30) days advance written notice to
Executive. If the Company elects to terminate Executive pursuant to this
Section 6.D prior to a Change in Control, the Company shall pay to Executive all
Accrued Compensation and shall continue to pay to Executive as provided herein
Executive's Salary for six (6) months from the date of such termination as
severance compensation. If the Company or its successor elects to terminate
Executive pursuant to this Section after a Change in Control, the Company (or
its successor) shall continue to pay to Executive as provided herein Executive's
Salary for eighteen (18) months from the date of such termination as severance
compensation. In addition, upon any termination under this Section 6.D., all of
the Executive's stock options granted prior to or on January 26, 2001 shall
become exercisable in full and all the shares of the common stock of the Company
awarded to Executive under the Company's 1997 Stock Incentive Plan and the 1993
Stock Option/Stock Issuance Plan prior to or on January 26, 2001 shall become
fully vested. Upon payment of the severance benefits described herein, all
obligations of the Company (or its successor) shall terminate.

    During the period when such severance compensation is being paid to
Executive, Executive shall not (i) engage, directly or indirectly, in any other
business activity that is competitive with, or that places him in a competing
position to that of the Company or any Affiliated Company (provided that
Executive may own less than two percent (2%) of the outstanding securities of
any publicly traded corporation), or (ii) hire, solicit, or attempt to hire on
behalf of himself or any other party any employee or exclusive consultant of the
Company. If the Company terminates this Agreement or the employment of Executive
with the Company other than pursuant to Section 6.A, 6.B or 6.C, then this
Section 6.D shall apply.

    E.  Constructive Termination.  In the event that the Company shall
materially reduce the powers and duties of employment of Executive resulting in
a material decrease in the responsibilities of Executive which are inconsistent
with Executive acting as President of the Company, such action shall be deemed
to be a termination of employment of Executive without cause pursuant to
Section 6.D. In the event of a Change in Control of the Company in which the
Company shall become a division or subsidiary of a larger organization,
references to the President of the Company shall be deemed to mean the President
of such division or subsidiary for purposes of this Section 6.E.

    1.  Change in Control.  For purposes of this Agreement, a "Change in
Control" shall have occurred if at any time during the term of Executive's
employment hereunder, any of the following events shall occur:

a.The consummation of a merger or consolidation of the Company with or into
another entity or any other corporate reorganization, if more than 50% of the
combined voting power of the continuing or surviving entity's securities
outstanding immediately after such merger, consolidation or other reorganization
is owned by persons who were not stockholders of the Company immediately prior
to such merger, consolidation or other reorganization;

b.A change in the composition of the Board, as a result of which fewer than
one-half of the incumbent directors are directors who either (1) had been
directors of the Company 24 months prior to such change; or (2) were elected, or
nominated for election, to the Board with the affirmative votes of at least a
majority of the directors who had been directors of the Company 24 months prior
to such change and who were still in office at the time of the election or
nomination; or

c.Any "person" (as such term is used in Section 13(d) and Section 14 of the
Exchange Act) by the acquisition of securities is or becomes the beneficial
owner, directly or indirectly, of securities of the Company representing 50% or
more of the combined voting power of

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the Company's then outstanding securities ordinarily (and apart from rights
accruing under special circumstances) having the right to vote at elections of
directors (the "Base Capital Stock") except that any change in the relative
beneficial ownership of the Company's securities resulting solely from a
reduction in the aggregate number of outstanding shares of Base Capital Stock,
and any decrease thereafter in such person's ownership of securities shall be
disregarded until such person increases in any manner, directly or indirectly,
such person's beneficial ownership of any securities of the Company. Thus, for
example, any person who owns less than 50% of the Company's outstanding shares,
shall cause a Change in Control to occur as of any subsequent date if such
person then acquires an additional interest in the Company which, when added to
the person's previous holdings, causes the person to hold more than 50% of the
Company's outstanding shares.

    The term "Change in Control" shall not include a transaction, the sole
purpose of which is to change the state of the Company's incorporation.

ARTICLE VII.

GENERAL PROVISIONS

    A.  Governing Law.  The validity, interpretation, construction and
performance of this Agreement and the rights of the parties thereunder shall be
interpreted and enforced under California law without reference to principles of
conflicts of laws. The parties expressly agree that inasmuch as the Company's
headquarters and principal place of business are located in California, it is
appropriate that California law govern this Agreement.

    B.  Assignment; Successors; Binding Agreement.  

    1.  Executive may not assign, pledge or encumber his interest in this
Agreement or any part thereof.

    2.  The Company will require any successor (whether direct or indirect, by
purchase, merger, consolidation or otherwise) to all or substantially all of the
business and/or assets of the Company, operation of law or by agreement in form
and substance reasonably satisfactory to Executive, to assume and agree to
perform this Agreement in the same manner and to the same extent that the
Company would be required to perform it if no such succession had taken place.

    3.  This Agreement shall inure to the benefit of and be enforceable by
Executive's personal or legal representatives, executors, administrators,
successors, heirs, distributee, devisees and legatees. If Executive should die
while any amount is at such time payable to him hereunder, all such amounts,
unless otherwise provided herein, shall be paid in accordance with the terms of
this Agreement to Executive's devisee, legates or other designee or, if there be
no such designee, to his estate.

    C.  No Waiver of Breach.  The waiver by any party of the breach of any
provision of this Agreement shall not be deemed to be a waiver of any subsequent
breach.

    D.  Notice.  For the purposes of this Agreement, notices and all other
communications provided for in this Agreement shall be in writing and shall be
deemed to have been duly given when delivered or mailed by certified or
registered mail, return receipt requested, postage prepaid, addressed to the
respective addresses set forth below or to such other address as either party
may have furnished to the

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other in writing in accordance herewith, except that notice of change of address
shall be effective only upon receipt.

  To the Company:   Nanogen, Inc.
10398 Pacific Center Court
San Diego, CA 92121
Attn: Chief Executive Officer  
To Executive:
 
Howard C. Birndorf
c/o Nanogen, Inc.
10398 Pacific Center Court
San Diego, CA 92121

    E.  Modification; Waiver; Entire Agreement.  No provisions of this Agreement
may be modified, waived or discharged unless such waiver, modification or
discharge is agreed to in writing signed by Executive and such officer as may be
specifically designated by the Board of the Company. No waiver by either party
hereto at any time of any breach by the other party of, or compliance with, any
condition or provision of this Agreement to be performed by such other party
shall be deemed a waiver of similar or dissimilar provisions or conditions at
the same or any prior or subsequent time. No agreements or representations, oral
or otherwise, express or implied, with respect to the subject matter hereof have
been made by either party which are not expressly set forth in this Agreement.

    F.  Validity.  The invalidity or unenforceability of any provision of this
Agreement shall not affect the validity or enforceability of any other provision
of this Agreement, which shall remain in full force and effect.

    G.  Controlling Document.  This Agreement supersedes any and all prior
employment agreements between the Company and Executive, but does not supersede
any other agreements between Company and Executive, including but not limited
to, the Nanogen Inc. Restricted Stock Purchase Agreement, any stock option
agreements or common stock purchase agreements entered into pursuant to the
Company's 1997 Stock Incentive Plan, the 1993 Stock Option/Stock Issuance Plan
and the Nanogen Employees' Handbook and Policies, except as expressly provided
herein. In case of conflict between any of the terms and conditions of this
Agreement and the documents herein referred to, the terms and conditions of this
Agreement shall control.

    H.  Executive Acknowledgment.  Executive acknowledges (a) that he has
consulted with or has had the opportunity to consult with independent counsel of
his own choice concerning this Agreement, and has been advised to do so by the
Company, and (b) that he has read and understands the Agreement, is fully aware
of its legal effect, and has entered into it freely based on his own judgment.

    I.  Remedies.  

    1.  Injunctive Relief.  The parties agree that the services to be rendered
by Executive hereunder are of a unique nature and that in the event of any
breach or threatened breach of any of the covenants contained herein, the damage
or imminent damage to the value and the goodwill of the Company's business will
be irreparable and extremely difficult to estimate, making any remedy at law or
in damages inadequate. Accordingly, the parties agree that the Company shall be
entitled to injunctive relief against Executive in the event of any breach or
threatened breach of any such provisions by Executive, in addition to any other
relief (including damages) available to the Company under this Agreement or
under law.

    2.  Exclusive.  Both parties agree that the remedy specified in
Section 7.I.1 above is not exclusive of any other remedy for the breach by
Executive of the terms hereof.

    J.  Counterparts.  This Agreement may be executed in one or more
counterparts, all of which taken together shall constitute one and the same
Agreement.

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    Executed by the parties as of the day and year first above written.

    NANOGEN, INC.
 
 
By:
/s/ V. RANDY WHITE   

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V. Randy White
Chief Executive Officer
 
 
EXECUTIVE:
 
 
By:
/s/ HOWARD C. BIRNDORF   

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Howard C. Birndorf

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QuickLinks

Exhibit 10.2

AMENDED AND RESTATED EMPLOYMENT AGREEMENT
ARTICLE I. TERM OF AGREEMENT
ARTICLE II. EMPLOYMENT DUTIES
ARTICLE III. COMPENSATION
ARTICLE IV. EXPENSE ALLOWANCES AND FRINGE BENEFITS
ARTICLE V. CONFIDENTIALITY
ARTICLE VI. TERMINATION
ARTICLE VII. GENERAL PROVISIONS