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                                                                Exhibit No. 10.8

                            INDEMNIFICATION AGREEMENT

        THIS INDEMNIFICATION AGREEMENT is made effective as of the 16th day of
April, 2002 (the "Agreement"), by and between NANOGEN, INC., a Delaware
corporation (the "Company") and ROBERT E. WHALEN (the "Indemnitee") with
reference to the following facts:

        WHEREAS, the Company desires the benefits of having Indemnitee serve as
an officer and/or director secure in the knowledge that any expenses, liability
and/or losses incurred by him in his good faith service to the Company will be
borne by the Company or its successors and assigns; and

        WHEREAS, Indemnitee is willing to serve in his position with the Company
only on the condition that he be indemnified for such expenses, liability and/or
losses; and

        WHEREAS, the Company and Indemnitee recognize the increasing difficulty
in obtaining liability insurance for directors, officers and agents of a
corporation at reasonable cost; and

        WHEREAS, the Company and Indemnitee recognize that there has been an
increase in litigation against corporate directors, officers and agents; and

        WHEREAS, the Company's Restated Certificate of Incorporation allows and
requires the Company to indemnify its directors, officers and agents to the
maximum extent permitted under Delaware law:

        NOW, THEREFORE, the parties hereby agree as follows:

        1.      DEFINITIONS. For purposes of this Agreement:

        1.1     "Agent" shall mean any person who (a) is or was a director,
officer, employee or agent of the Company or a subsidiary of the Company whether
serving in such capacity or as a director, officer, employee, agent, fiduciary
or other official of another corporation, joint venture, trust or other
enterprise at the request of, for the convenience of, or to represent the
interests of the Company or a subsidiary of the Company or (b) was a director,
officer, employee or agent of Nanogen, Inc., a California corporation and the
predecessor by merger to the Company (the "Predecessor Corporation"), whether
serving in such capacity or as a director, officer, employee, agent, fiduciary
or other official of another corporation, joint venture, trust or other
enterprise at the request of, for the convenience of, or to represent the
interests of such Predecessor Corporation.

        1.2     "Change of Control" shall mean the occurrence of any of the
following events after the date of this Agreement:

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        (a)     A change in the composition of the board of directors of the
Company (the "Board"), as a result of which fewer than two-thirds of the
incumbent directors are directors who either (a) had been directors of the
Company 24 months prior to such change or (b) 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

        (b)     Any "person" (as such term is used in sections 13(d) and 14(d)
of the Securities Exchange Act of 1934 (the "Exchange Act"), as amended) through
the acquisition or aggregation of securities is or becomes the beneficial owner,
directly or indirectly, of securities of the Company representing 20 percent or
more of the combined voting power of 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 "Capital Stock"); PROVIDED,
HOWEVER, that any change in ownership of the Company's securities by any person
resulting solely from a reduction in the aggregate number of outstanding shares
of 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.

        1.3     "Disinterested Director" shall mean a director of the Company
who is not and was not a party to the Proceeding in respect of which
indemnification is being sought by Indemnitee.

        1.4     "Expenses" shall be broadly construed and shall include, without
limitation, (a) all direct and indirect costs incurred, paid or accrued, (b) all
attorneys' fees, retainers, court costs, transcripts, fees of experts, witness
fees, travel expenses, food and lodging expenses while traveling, duplicating
costs, printing and binding costs, telephone charges, postage, delivery service,
freight or other transportation fees and expenses, (c) all other disbursements
and out-of-pocket expenses, (d) amounts paid in settlement, to the extent not
prohibited by Delaware Law, and (e) reasonable compensation for time spent by
Indemnitee for which he is otherwise not compensated by the Company or any third
party, actually and reasonably incurred in connection with or arising out of a
Proceeding, including a Proceeding by Indemnitee to establish or enforce a right
to indemnification under this Agreement, applicable law or otherwise.

        1.5     "Independent Counsel" shall mean a law firm or a member of a law
firm that neither is presently nor in the past five years has been retained to
represent: (a) the Company, an affiliate of the Company or Indemnitee in any
matter material to either party or (b) any other party to the Proceeding giving
rise to a claim for indemnification hereunder. Notwithstanding the foregoing,
the term "Independent Counsel" shall not include any person who, under the
applicable standards of professional conduct then prevailing, would have a
conflict of interest in representing either the Company or Indemnitee in an
action to determine Indemnitee's right to indemnification under this Agreement.

        1.6     "Liabilities" shall mean liabilities of any type whatsoever,
including, but not limited to, judgments or fines, ERISA or other excise taxes
and penalties, and amounts paid in settlement (including all interest,
assessments or other charges paid or payable in connection with

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any of the foregoing) actually and reasonably incurred by Indemnitee in
connection with a Proceeding.

        1.7     "Delaware Law" means the Delaware General Corporation Law, as
amended and in effect from time to time, or any successor or other statutes of
Delaware having similar import and effect.

        1.8     "Proceeding" shall mean any pending, threatened or completed
action, hearing, suit or any other proceeding, whether civil, criminal,
arbitrative, administrative, investigative or any alternative dispute resolution
mechanism, including without limitation any such Proceeding brought by or in the
right of the Company.

        2.      EMPLOYMENT RIGHTS AND DUTIES. Subject to any other obligations
imposed on either of the parties by contract or by law, and with the
understanding that this Agreement is not intended to confer employment rights on
either party which they did not possess on the date of its execution, Indemnitee
agrees to serve as a director or officer so long as he is duly appointed or
elected and qualified in accordance with the applicable provisions of the
Restated Certificate of Incorporation (the "Certificate") and Bylaws (the
"Bylaws") of the Company or any subsidiary of the Company and until such time as
he resigns or fails to stand for election or until his employment terminates.
Indemnitee may from time to time also perform other services at the request, or
for the convenience of, or otherwise benefiting the Company. Indemnitee may at
any time and for any reason resign or be removed from such position (subject to
any other contractual obligation or other obligation imposed by operation of
law), in which event the Company shall have no obligation under this Agreement
to continue Indemnitee in any such position.

        2.1     DIRECTORS' AND OFFICERS' INSURANCE.

        (a)     The Company hereby covenants and agrees that, so long as
Indemnitee shall continue to serve as a director or officer of the Company and
thereafter so long as Indemnitee shall be subject to any possible Proceeding,
the Company, subject to Section 2.1(c), shall maintain directors' and officers'
insurance in full force and effect.

        (b)     In all policies of directors' and officers' insurance,
Indemnitee shall be named as an insured in such a manner as to provide
Indemnitee the same rights and benefits, subject to the same limitations, as are
accorded to the Company's directors or officers most favorably insured by such
policy.

        (c)     The Company shall have no obligation to maintain directors' and
officers' insurance if the Company determines in good faith that such insurance
is not reasonably available, the premium costs for such insurance are
disproportionate to the amount of coverage provided, or the coverage provided by
such insurance is limited by exclusions so as to provide an insufficient
benefit.

        3.      INDEMNIFICATION. The Company shall indemnify Indemnitee to the
fullest extent authorized or permitted by Delaware Law and the provisions of the
Certificate and Bylaws of the Company in effect on the date hereof, and as
Delaware Law, the Certificate and Bylaws may

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from time to time be amended (but, in the case of any such amendment, only to
the extent such amendment permits the Company to provide broader indemnification
rights than Delaware Law, the Certificate and/or Bylaws permitted the Company to
provide before such amendment). The right to indemnification conferred in the
Certificate shall be presumed to have been relied upon by Indemnitee in serving
or continuing to serve the Company as a director or officer and shall be
enforceable as a contract right. Without in any way diminishing the scope of the
indemnification provided by the Certificate and this Section 3, the Company
shall indemnify Indemnitee if and whenever he is or was a witness, party or is
threatened to be made a witness or a party to any Proceeding, by reason of the
fact that he is or was an Agent or by reason of anything done or not done, or
alleged to have been done or not done, by him in such capacity, against all
Expenses and Liabilities actually and reasonably incurred by Indemnitee or on
his behalf in connection with the investigation, defense, settlement or appeal
of such Proceeding. In addition to, and not as a limitation of, the foregoing,
the rights of indemnification of Indemnitee provided under this Agreement shall
include those rights set forth in Sections 4, 5 and 6 below.

        4.      PAYMENT OF EXPENSES.

        4.1     All Expenses incurred by or on behalf of Indemnitee shall be
advanced by the Company to Indemnitee within 20 days after the receipt by the
Company of a written request for such advance which may be made from time to
time, whether prior to or after final disposition of a Proceeding (unless there
has been a final determination by a court of competent jurisdiction that
Indemnitee is not entitled to be indemnified for such Expenses). Indemnitee's
entitlement to advancement of Expenses shall include those incurred in
connection with any Proceeding by Indemnitee seeking a determination, an
adjudication or an award in arbitration pursuant to this Agreement. The requests
shall reasonably evidence the Expenses incurred by Indemnitee in connection
therewith. Indemnitee hereby undertakes to repay the amounts advanced if it
shall ultimately be determined that Indemnitee is not entitled to be indemnified
pursuant to the terms of this Agreement.

        4.2     Notwithstanding any other provision in this Agreement, to the
extent that Indemnitee has been successful on the merits or otherwise in defense
of any Proceeding, Indemnitee shall be indemnified against all Expenses actually
and reasonably incurred by Indemnitee in connection therewith.

        5.      PROCEDURE FOR DETERMINATION OF ENTITLEMENT TO INDEMNIFICATION.

        5.1     Whenever Indemnitee believes that he is entitled to
indemnification pursuant to this Agreement, Indemnitee shall submit a written
request for indemnification (the "Indemnification Request") to the Company to
the attention of the President with a copy to the Secretary. This request shall
include documentation or information which is necessary for the determination of
entitlement to indemnification and which is reasonably available to Indemnitee.
Determination of Indemnitee's entitlement to indemnification shall be made no
later than 60 days after receipt of the Indemnification Request. The President
or the Secretary shall, promptly upon receipt of Indemnitee's request for
indemnification, advise the Board in writing that Indemnitee has made such
request for indemnification.

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        5.2     The Indemnification Request shall set forth Indemnitee's
selection of which of the following forums shall determine whether Indemnitee is
entitled to indemnification:

                (1)    A majority vote of Directors who are not parties to the
action with respect to which indemnification is sought, even though less than a
quorum.

                (2)    A written opinion of an Independent Counsel (provided
there are no such Directors as set forth in (1) above or if such Directors as
set forth in (1) above so direct).

                (3)    A majority vote of the stockholders at a meeting at which
a quorum is present, with the shares owned by the person to be indemnified not
being entitled to vote thereon.

                (4)    The court in which the Proceeding is or was pending upon
application by Indemnitee.

        The Company agrees to bear any and all costs and expenses incurred by
Indemnitee or the Company in connection with the determination of Indemnitee's
entitlement to indemnification by any of the above forums.

        6.      PRESUMPTIONS AND EFFECT OF CERTAIN PROCEEDINGS. No initial
finding by the Board, its counsel, Independent Counsel, arbitrators or the
stockholders shall be effective to deprive Indemnitee of the protection of this
indemnity, nor shall a court or other forum to which Indemnitee may apply for
enforcement of this indemnity give any weight to any such adverse finding in
deciding any issue before it. Upon making a request for indemnification,
Indemnitee shall be presumed to be entitled to indemnification under this
Agreement and the Company shall have the burden of proof to overcome that
presumption in reaching any contrary determination. The termination of any
Proceeding by judgment, order, settlement, arbitration award or conviction, or
upon a plea of NOLO CONTENDERE or its equivalent, shall not, of itself, (a)
adversely affect the rights of Indemnitee to indemnification except as
indemnification may be expressly prohibited under this Agreement, (b) create a
presumption that Indemnitee did not act in good faith and in a manner which he
reasonably believed to be in or not opposed to the best interests of the Company
or (c) with respect to any criminal action or proceeding, create a presumption
that Indemnitee had reasonable cause to believe that his conduct was unlawful.

        7.      REMEDIES OF INDEMNITEE IN CASES OF DETERMINATION NOT TO
                INDEMNIFY OR TO ADVANCE EXPENSES.

        7.1     In the event that (a) an initial determination is made that
Indemnitee is not entitled to indemnification, (b) advances for Expenses are not
made when and as required by this Agreement, (c) payment has not been timely
made following a determination of entitlement to indemnification pursuant to
this Agreement or (d) Indemnitee otherwise seeks enforcement of this Agreement,
Indemnitee shall be entitled to a final adjudication in an appropriate court of
the State of Delaware of his entitlement to such indemnification or advance.
Alternatively, Indemnitee at his option may seek an award in arbitration. If the
parties are unable to agree on an arbitrator, the parties shall provide JAMS
Endispute ("JAMS") with a statement of the nature of the dispute and the desired
qualifications of the arbitrator. JAMS will then provide a list of three

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available arbitrators. Each party may strike one of the names on the list, and
the remaining person will serve as the arbitrator. If both parties strike the
same person, JAMS will select the arbitrator from the other two names. The
arbitration award shall be made within 90 days following the demand for
arbitration. Except as set forth herein, the provisions of Delaware law shall
apply to any such arbitration. The Company shall not oppose Indemnitee's right
to seek any such adjudication or arbitration award. In any such proceeding or
arbitration Indemnitee shall be presumed to be entitled to indemnification under
this Agreement and the Company shall have the burden of proof to overcome that
presumption.

        7.2     An initial determination, in whole or in part, that Indemnitee
is not entitled to indemnification shall create no presumption in any judicial
proceeding or arbitration that Indemnitee has not met the applicable standard of
conduct for, or is otherwise not entitled to, indemnification.

        7.3     If an initial determination is made or deemed to have been made
pursuant to the terms of this Agreement that Indemnitee is entitled to
indemnification, the Company shall be bound by such determination in the absence
of (a) a misrepresentation of a material fact by Indemnitee in the request for
indemnification or (b) a specific finding (which has become final) by a court of
competent jurisdiction that all or any part of such indemnification is expressly
prohibited by law.

        7.4     The Company and Indemnitee agree herein that a monetary remedy
for breach of this Agreement, at some later date, will be inadequate,
impracticable and difficult of proof, and further agree that such breach would
cause Indemnitee irreparable harm. Accordingly, the Company and Indemnitee agree
that Indemnitee shall be entitled to temporary and permanent injunctive relief
to enforce this Agreement without the necessity of proving actual damages or
irreparable harm. The Company and Indemnitee further agree that Indemnitee shall
be entitled to such injunctive relief, including temporary restraining orders,
preliminary injunctions and permanent injunctions, without the necessity of
posting bond or other undertaking in connection therewith. Any such requirement
of bond or undertaking is hereby waived by the Company, and the Company
acknowledges that in the absence of such a waiver, a bond or undertaking may be
required by the court.

        7.5     The Company shall be precluded from asserting that the
procedures and presumptions of this Agreement are not valid, binding and
enforceable. The Company shall stipulate in any such court or before any such
arbitrator that the Company is bound by all the provisions of this Agreement and
is precluded from making any assertion to the contrary.

        7.6     Expenses incurred by Indemnitee in connection with his request
for indemnification under, seeking enforcement of or to recover damages for
breach of this Agreement shall be borne and advanced by the Company.

        8.      OTHER RIGHTS TO INDEMNIFICATION. Indemnitee's rights of
indemnification and advancement of expenses provided by this Agreement shall not
be deemed exclusive of any other rights to which Indemnitee may now or in the
future be entitled under applicable law, the

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Certificate, the Bylaws, an employment agreement, a vote of stockholders or
Disinterested Directors, insurance or other financial arrangements or otherwise.

        9.      LIMITATIONS ON INDEMNIFICATION. No indemnification pursuant to
Section 3 shall be paid by the Company nor shall Expenses be advanced pursuant
to Section 3:

        9.1     INSURANCE. To the extent that Indemnitee is reimbursed pursuant
to such insurance as may exist for Indemnitee's benefit. Notwithstanding the
availability of such insurance, Indemnitee also may claim indemnification from
the Company pursuant to this Agreement by assigning to the Company any claims
under such insurance to the extent Indemnitee is paid by the Company. Indemnitee
shall reimburse the Company for any sums he receives as indemnification from
other sources to the extent of any amount paid to him for that purpose by the
Company;

        9.2     SECTION 16(b). On account and to the extent of any wholly or
partially successful claim against Indemnitee for an accounting of profits made
from the purchase or sale by Indemnitee of securities of the Company pursuant to
the provisions of Section 16(b) or the Securities Exchange Act of 1934, as
amended, and amendments thereto or similar provisions of any federal, state or
local statutory law; or

        9.3     INDEMNITEE'S PROCEEDINGS. Except as otherwise provided in this
Agreement, in connection with all or any part of a Proceeding which is initiated
or maintained by or on behalf of Indemnitee, or any Proceeding by Indemnitee
against the Company or its directors, officers, employees or other agents,
unless (a) such indemnification is expressly required to be made by Delaware
Law, (b) the Proceeding was authorized by a majority of the Disinterested
Directors, (c) there has been a Change of Control or (d) such indemnification is
provided by the Company, in its sole discretion, pursuant to the powers vested
in the Company under Delaware Law.

        10.     DURATION AND SCOPE OF AGREEMENT; BINDING EFFECT. This Agreement
shall continue so long as Indemnitee shall be subject to any possible Proceeding
subject to indemnification by reason of the fact that he is or was an Agent and
shall be applicable to Proceedings commenced or continued after execution of
this Agreement, whether arising from acts or omissions occurring before or after
such execution. This Agreement shall be binding upon the Company and its
successors and assigns (including any direct or indirect successor by purchase,
merger, consolidation or otherwise to all or substantially all of the business
or assets of the Company) and shall inure to the benefit of Indemnitee and his
spouse, assigns, heirs, devisees, executors, administrators and other legal
representatives.

        11.     NOTICE BY INDEMNITEE AND DEFENSE OF CLAIMS. Indemnitee agrees
promptly to notify the Company in writing upon being served with any summons,
citation, subpoena, complaint, indictment, information or other document
relating to any matter which may be subject to indemnification hereunder,
whether civil, criminal, arbitrative, administrative or investigative;

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but the omission so to notify the Company will not relieve it from any liability
which it may have to Indemnitee if such omission does not actually prejudice the
Company's rights and, if such omission does prejudice the Company's rights, it
will relieve the Company from liability only to the extent of such prejudice;
nor will such omission relieve the Company from any liability which it may have
to Indemnitee otherwise than under this Agreement. With respect to any
Proceeding:

                (a)    The Company will be entitled to participate therein at
its own expense;

                (b)    Except as otherwise provided below, to the extent that it
may wish, the Company jointly with any other indemnifying party similarly
notified will be entitled to assume the defense thereof, with counsel reasonably
satisfactory to Indemnitee. After notice from the Company to Indemnitee of its
election so to assume the defense thereof and the assumption of such defense,
the Company will not be liable to Indemnitee under this Agreement for any
attorney fees or costs subsequently incurred by Indemnitee in connection with
Indemnitee's defense except as otherwise provided below. Indemnitee shall have
the right to employ his counsel in such Proceeding but the fees and expenses of
such counsel incurred after notice from the Company of its assumption of the
defense thereof and the assumption of such defense shall be at the expense of
Indemnitee unless (i) the employment of counsel by Indemnitee has been
authorized by the Company, (ii) Indemnitee shall have reasonably concluded that
there may be a conflict of interest between the Company and Indemnitee in the
conduct of the defense of such action or that the Company's counsel may not be
adequately representing Indemnitee or (iii) the Company shall not in fact have
employed counsel to assume the defense of such action, in each of which cases
the fees and expenses of counsel shall be at the expense of the Company; and

                (c)    The Company shall not be liable to indemnify Indemnitee
under this Agreement for any amounts paid in settlement of any action or claim
effected without its written consent. The Company shall not settle any action or
claim which would impose any limitation or penalty on Indemnitee without
Indemnitee's written consent. Neither the Company nor Indemnitee will
unreasonably withhold its or his consent to any proposed settlement.

        11.1    CONTRIBUTION. In order to provide for just and equitable
contribution in circumstances in which the indemnification provided for in this
Agreement is held by a court of competent jurisdiction to be unavailable to
Indemnitee in whole or part, the Company shall, in such an event, after taking
into account, among other things, contributions by other directors and officers
of the Company pursuant to indemnification agreements or otherwise, and, in the
absence of personal enrichment, acts of intentional fraud or dishonesty or
criminal conduct on the part of Indemnitee, contribute to the payment of
Indemnitee's losses to the extent that, after other contributions are taken into
account, such losses exceed: (i) in the case of a director of the Company or any
of its subsidiaries who is not an officer of the Company or any of such
subsidiaries, the amount of fees paid to the director for serving as a director
during the 12 months preceding the commencement of the Proceeding; or (ii) in
the case of a director of the Company or any of its subsidiaries who is also an
officer of the Company or any of such subsidiaries, the amount set forth in
clause (i) plus 5% of the aggregate cash compensation paid to said director for
service in such office(s) during the 12 months preceding the commencement of the
Proceeding; or (iii) in the case of an officer of the Corporation or any of its
subsidiaries, 5% of

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the aggregate cash compensation paid to such officer for service in such
office(s) during the 12 months preceding the commencement of such Proceeding.

        12.     ESTABLISHMENT OF TRUST. In order to secure the obligations of
the Company to indemnify and to advance Expenses to Indemnitee pursuant to this
Agreement, upon a Change of Control of the Company, the Company or its successor
or assign shall establish a Trust (the "Trust") for the benefit of the
Indemnitee, the trustee (the "Trustee") of which shall be chosen by the Company
and which is reasonably acceptable to the Indemnitee. Thereafter, from time to
time, upon receipt of a written request from Indemnitee, the Company shall fund
the Trust in amounts sufficient to satisfy any and all Liabilities and Expenses
reasonably anticipated at the time of such request for which the Company may
indemnify Indemnitee hereunder. The amount or amounts to be deposited in the
Trust pursuant to the foregoing funding obligation shall be determined by mutual
agreement of the Indemnitee and the Company or, if the Company and the
Indemnitee are unable to reach such an agreement, by Independent Counsel
selected jointly by the Company and the Indemnitee. The terms of the Trust shall
provide that except upon the consent of the Indemnitee and the Company, (i) the
Trust shall not be revoked or the principal thereof invaded, without the written
consent of the Indemnitee, (ii) the Trustee shall advance to the Indemnitee,
within 20 days of a request by the Indemnitee, any and all Expenses, the
Indemnitee hereby agreeing to reimburse the Trustee of the Trust for all
Expenses so advanced if a final determination is made by a court in a final
adjudication from which there is no further right of appeal that the Indemnitee
is not entitled to be indemnified under this Agreement, (iii) the Trust shall
continue to be funded by the Company in accordance with the funding obligations
set forth in this Section, (iv) the Trustee shall promptly pay to the Indemnitee
any amounts to which the Indemnitee shall be entitled pursuant to this
Agreement, and (v) all unexpended funds in the Trust shall revert to the Company
upon a final determination by Independent Counsel selected by Indemnitee or a
court of competent jurisdiction that Indemnitee has been fully indemnified with
respect to the Proceeding giving rise to the funding of the Trust under the
terms of this Agreement. The establishment of the Trust shall not, in any way,
diminish the Company's obligation to indemnify Indemnitee against Expenses and
Liabilities to the full extent required by this Agreement.

        13.     MISCELLANEOUS PROVISIONS.

        13.1    SEVERABILITY; PARTIAL INDEMNITY. If any provision or provisions
of this Agreement (or any portion thereof) shall be held by a court of competent
jurisdiction to be invalid, illegal or unenforceable for any reason whatever:
(a) such provision shall be limited or modified in its application to the
minimum extent necessary to avoid the invalidity, illegality or unenforceability
of such provision; (b) the validity, legality and enforceability of the
remaining provisions of this Agreement shall not in any way be affected or
impaired thereby; and (c) to the fullest extent possible, the provisions of this
Agreement shall be construed so as to give effect to the intent manifested by
the provision (or portion thereof) held invalid, illegal or unenforceable. If
Indemnitee is entitled under any provision of this Agreement to indemnification
by the Company for some or a portion of any Expenses or Liabilities of any type
whatsoever incurred by him in the investigation, defense, settlement or appeal
of a Proceeding but not entitled to all of the total amount thereof, the Company
shall nevertheless indemnify Indemnitee for such total amount

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except as to the portion thereof for which it has been determined pursuant to
Section 5 hereof that Indemnitee is not entitled.

        13.2    IDENTICAL COUNTERPARTS. This Agreement may be executed in one or
more counterparts, each of which shall for all purposes be deemed to be an
original but all of which together shall constitute one and the same Agreement.
Only one such counterpart signed by the party against whom enforceability is
sought needs to be produced to evidence the existence of this Agreement.

        13.3    INTERPRETATION OF AGREEMENT. It is understood that the parties
hereto intend this Agreement to be interpreted and enforced so as to provide
indemnification to Indemnitee to the fullest extent not now or hereafter
prohibited by law.

        13.4    HEADINGS. The headings of the Sections and paragraphs of this
Agreement are inserted for convenience only and shall not be deemed to
constitute part of this Agreement or to affect the construction thereof.

        13.5    PRONOUNS. Use of the masculine pronoun shall be deemed to
include use of the feminine pronoun where appropriate.

        13.6    MODIFICATION AND WAIVER. No supplement, modification or
amendment of this Agreement shall be binding unless executed in writing by both
of the parties to this Agreement. No waiver of any provision of this Agreement
shall be deemed to constitute a waiver of any of the provisions hereof (whether
or not similar) nor shall such waiver constitute a continuing waiver. No waiver
of any provision of this Agreement shall be effective unless executed in
writing.

        13.7    NOTICES. All notices, requests, demands and other communications
hereunder shall be in writing and shall be deemed to have been duly given if (i)
delivered by hand and receipted for by the party to whom said notice or other
communication shall have been directed or (ii) mailed by certified or registered
mail with postage prepaid, on the third business day after the date on which it
is so mailed:

        (a)     If to Indemnitee, to:

                Robert E. Whalen
                Nanogen, Inc.
                10398 Pacific Center Court
                San Diego, California 92121
                Telephone: (858) 410-4600
                Telefax:   (858) 410-4949

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        (b)     If to the Company to:

                Nanogen, Inc.
                10398 Pacific Center Court
                San Diego, California 92121
                Telephone: (858) 410-4600
                Telefax:   (889) 410-4949
                Attention: Chief Executive Officer

or to such other address as may have been furnished to Indemnitee by the Company
or to the Company by Indemnitee, as the case may be.

        13.8    GOVERNING LAW. The parties agree that this Agreement shall be
governed by, and construed and enforced in accordance with, the laws of the
State of Delaware, as applied to contracts between Delaware residents entered
into and to be performed entirely within Delaware.

        13.9    CONSENT TO JURISDICTION. The Company and Indemnitee each hereby
irrevocably consent to the jurisdiction of the courts of the State of Delaware
for all purposes in connection with any action or proceeding which arises out of
or relates to this agreement and agree that any action instituted under this
agreement shall be brought only in the state courts of the State of Delaware.

        13.10   ENTIRE AGREEMENT. This Agreement represents the entire agreement
between the parties hereto, and there are no other agreements, contracts or
understanding between the parties hereto with respect to the subject matter of
this Agreement, except as specifically referred to herein or as provided in
Sections 8 and 2.1 hereof.

        IN WITNESS WHEREOF, the parties hereto have executed this Agreement on
the day and year first above written.

                                            NANOGEN, INC.

                                            By: /s/ V. Randy White
                                                --------------------------------
                                                 V. Randy White
                                                 Chief Executive Officer

                                            INDEMNITEE

                                            /s/ Robert E. Whalen
                                            ------------------------------------
                                                 Robert E. Whalen

                                  Page 11 of 11<Page>

                                                                    Exhibit 10.9

NEITHER THIS WARRANT NOR THE SHARES OF STOCK ISSUABLE UPON EXERCISE HEREOF, HAVE
BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED. NO SALE, TRANSFER
OR OTHER DISPOSITION OF THIS WARRANT OR SAID SHARES MAY BE EFFECTED WITHOUT (i)
AN EFFECTIVE REGISTRATION STATEMENT RELATED THERETO, (ii) AN OPINION OF COUNSEL
FOR THE HOLDER, REASONABLY SATISFACTORY OR (iii) RECEIPT OF A NO-ACTION LETTER
FROM THE SECURITIES AND EXCHANGE COMMISSION TO THE EFFECT THAT REGISTRATION
UNDER THE ACT IS NOT REQUIRED.

Shares Issuable Upon Exercise:  Up to 50,000

                        WARRANT TO PURCHASE COMMON STOCK
                                       OF
                                  NANOGEN, INC.

                             EXPIRES APRIL 12, 2007

     THIS CERTIFIES THAT, for value received, GeneType AG, a wholly-owned
Australian corporate subsidiary of Genetic Technologies Limited, having an
office at 60-66 Hanover Street, Fitzroy, Victoria 3065, Australia ("GeneType")
or its registered assigns (GeneType or its registered assigns shall hereinafter
be referred to as "HOLDER"), is entitled, subject to the terms and conditions
set forth below, to subscribe for and purchase up to 50,000 shares (as adjusted
pursuant to the provisions hereof, the "SHARES") of the fully paid and
nonassessable common stock ("COMMON STOCK"), par value $.001 per share, of
Nanogen, Inc., a Delaware corporation (the "COMPANY") at an exercise price per
share of $4.10 (such price and such other price as shall result, from time to
time, from adjustments specified herein is referred to as the "EXERCISE PRICE").
The term "WARRANT" as used herein shall mean this Warrant, and any warrants
delivered in substitution or exchange therefor as provided herein. This Warrant
is being issued pursuant to the License Agreement between GeneType and the
Company, dated April 12, 2002 (the "LICENSE AGREEMENT")

     1.   TERM. Subject to the terms and conditions set forth herein, this
Warrant is exercisable, in whole or in part, at any time and from time to time
from and after April 12, 2002 (the "GRANT DATE") and prior to 5:00 p.m., Pacific
Standard Time on the date above that is the fifth anniversary of the Grant Date
(the "EXERCISE PERIOD") and shall be void thereafter.

     2.   METHOD OF EXERCISE; NET ISSUE EXERCISE.

     (a)  METHOD OF EXERCISE; PAYMENT; ISSUANCE OF NEW WARRANT. This Warrant may
be exercised by the Holder, by either, at the election of the Holder, (i) the
surrender of this Warrant to the Company (with the Notice of Exercise attached
hereto as Exhibit A-1 duly completed and executed on behalf of the Holder), at
the principal office of the Company and by payment to the Company, for the
account of the Company, by check or wire transfer of immediately available funds
to a bank account specified by the Company, of an amount equal to the Exercise
Price multiplied by the number of Shares then being purchased as specified in
the Exercise Form in

                                       -1-
<Page>

lawful money of the United States of America or (ii) if in connection with a
registered public offering of the Company's securities, the surrender of this
Warrant (with the Notice of Exercise attached hereto as Exhibit A-2 duly
completed and executed on behalf of Holder) at the principal office of the
Company and by payment to the Company, for the account of the Company, by check,
wire transfer of immediately available funds to a bank account specified by the
Company or from the proceeds of the sale of Shares to be sold by the Holder in
such public offering of an amount equal to the Exercise Price multiplied by the
number of Shares then being purchased as specified in the Exercise Form in
lawful money of the United States of America. The Company agrees that such
Shares shall be deemed to be issued to the Holder as the record holder of such
Shares as of the close of business on the date on which this Warrant shall have
been surrendered and payment made for the Shares as aforesaid (the "EXERCISE
DATE"). A stock certificate or certificates for the Shares specified in the
Notice of Exercise shall be delivered to the Holder as soon as practicable, and
in any event within 30 days thereafter. If this Warrant shall have been
exercised only in part, the Company shall, at the time of delivery of the stock
certificate or certificates, deliver to the Holder a new Warrant evidencing the
rights to purchase the remaining Shares, which new Warrant shall in all other
respects be identical with this Warrant. No adjustments shall be made on Shares
issuable on the exercise of this Warrant for any cash dividends paid or payable
to holders of record of common stock prior to the date as of which the Holder
shall be deemed to be the record holder of such Shares. However, the number of
Shares shall be adjusted to reflect any stock dividend, stock split or other
conversion of the number of shares of the Company into a different number of
shares, however denominated, as described in Section 3.

     (b)  NET ISSUE EXERCISE. In lieu of exercising this Warrant pursuant to
Section 2(a), the Holder may elect to receive, without payment by the Holder of
any additional consideration, shares equal to the value of this Warrant or any
portion hereof by the surrender of this Warrant or such portion to the Company
(with the Notice of Exercise attached hereto as Exhibit A-1 hereto duly
completed and executed) at the principal office of the Company. Thereupon, the
Company shall issue to the Holder such number of fully paid and nonassessable
shares of Common Stock as is computed using the following formula:

                                   X = Y (A-B)
                                       -------
                                          A

               where

                    X  =  the number of shares to be issued to the Holder
                          pursuant to this Section 2(b).

                    Y  =  the number of shares of common stock otherwise
                          issuable under this Warrant (as adjusted to the date
                          of such calculation).

                    A  =  the closing stock price of one share of the Company's
                          common stock as reported by the Nasdaq National Market
                          the business day immediately prior to the Exercise.

                                       -2-
<Page>

                    B  =  the Exercise Price in effect under this Warrant at the
                          time the net issue election is made pursuant to this
                          Section 2(b).

     3.   ADJUSTMENT OF WARRANT PRICE AND NUMBER OF SHARES. The number and kind
of securities purchasable upon the exercise of the Warrant and the Warrant Price
shall be subject to adjustment from time to time upon the occurrence of certain
events, as follows:

     (a)  RECLASSIFICATION OR MERGER. In case of any reclassification, change or
conversion of securities of the class issuable upon exercise of this Warrant
(other than a change in par value, or from par value top no par value, or from
no par value to par value, or as a result of a subdivision or combination), or
in case of any merger of the Company with or into another corporation (other
than a merger with another corporation in which the Company is a continuing
corporation and which does not result in any reclassification or change of
outstanding securities issuable upon exercise of this Warrant), or in case of
any sale of all or substantially all of the assets of the Company, the Company,
or such successor or purchasing corporation, as the case may be, shall execute a
new Warrant) providing that the Holder of this Warrant shall have the right to
exercise such new Warrant and upon such exercise to receive, in lieu of each
share of Common Stock theretofore issuable upon exercise of this Warrant, the
kind and amount of shares of stock, other securities, money and property
receivable upon such reclassification, change or merger by a holder of one share
of Common Stock. Such new Warrant shall provide for adjustments that shall be as
nearly equivalent as may be practicable to the adjustments provided for in this
Section 3. The provisions of this Section 3(a) shall similarly apply to
successive reclassification, changes, mergers and transfers.

     (b)  SUBDIVISIONS OR COMBINATION OF SHARES. If the Company at any time
while this Warrant remains outstanding and unexpired shall subdivide or combine
its Common Stock, the Warrant Price and the number of shares issuable upon
exercise hereof shall be proportionately adjusted.

     (c)  STOCK DIVIDENDS. If the Company at any time while this Warrant is
outstanding and unexpired shall pay a dividend payable in shares of Common Stock
(except any distribution specifically provided for in Sections 3 (a) and (b)),
then the Warrant Price shall be adjusted, from and after the date of
determination of stockholders entitled to receive such dividend or distribution,
to that price determined by multiplying the Warrant Price in effect immediately
prior to such date of determination by a fraction (i) the numerator of which
shall be the total number of shares of Common Stock outstanding immediately
prior to such dividend or distribution, and (ii) the denominator of which shall
immediately after such dividend or distribution and the number of Shares subject
to this Warrant against impairment.

     (d)  NO IMPAIRMENT. The Company will not, by amendment of its Certificate
of Incorporation or through any reorganization, recapitalization, transfer of
assets, consolidation, merger, dissolution, issue or sale of securities or any
other voluntary action, avoid or seek to avoid the observance or performance of
any of the terms to be observed or performed hereunder by the Company, but will
at all times in good faith assist in the carrying out of all the provisions

                                       -3-
<Page>

of this Section 3 and in the taking of all such actions as may be necessary or
appropriate in order to protect the rights of the holder of this warrant against
impairment.

     (e)  NOTICES OF RECORD DATE. In any event in any taking of the Company of a
record of its stockholders for the purpose of determining stockholders who are
entitled to receive payment of any dividend (other than cash dividend) or other
distribution, any right to subscribe for, purchase or otherwise acquire any
share of any class or any other securities or property, or to receive any other
right, or for the purpose of determining stockholders who are entitled to vote
in connection with any proposed merger or consolidation of the Company with or
into any other corporation, or any proposed sale, lease or conveyance of all or
substantially all of the assets of the Company, or any proposed liquidation,
dissolution or winding up of the Company, the Company shall mail to the Holder
of the Warrant, at least 20 days prior to the date specified therein, a notice
specifying the date on which any such record is to be taken for the purpose of
such dividend, distribution or right, and the amount and character of such
dividend, distribution or right.

     4.   NOTICE OF ADJUSTMENTS. Whenever the Warrant Price shall be adjusted
pursuant to the provisions hereof, the Company shall within 20 days of such
adjustment deliver a certificate signed by its chief financial officer to the
registered holder(s) hereof setting forth, in reasonable detail, the event
requiring the adjustment, the amount of the adjustment, the method by which such
adjustment was calculated, and the Warrant Price after giving effect to such
adjustment.

     5.   NO FRACTIONAL SHARES OR SCRIP. No fractional shares or scrip
representing fractional shares shall be issued upon the exercise of this
Warrant. In lieu of any fractional share to which the Holder would otherwise be
entitled, the Company shall make a cash payment equal to the Exercise Price
multiplied by such fraction.

     6.   REPLACEMENT OF WARRANT. On receipt of evidence reasonably satisfactory
to the Company of the loss, theft, destruction or mutilation of this Warrant
and, in the case of loss, theft or destruction, on delivery of an indemnity
agreement reasonably satisfactory in form and substance to the Company or, in
the case of mutilation, on surrender and cancellation of this Warrant, the
Company at its expense shall execute and deliver, in lieu of this Warrant, a new
warrant of like tenor and amount.

     7.   RIGHTS OF STOCKHOLDERS. The Holder of this Warrant shall not be
entitled to vote or receive dividends or be deemed the holder of common stock
nor shall anything contained herein be construed to confer upon the Holder, as
such, any of the rights of a stockholder of the Company or any right to vote for
the election of directors or upon any matter submitted to stockholders at any
meeting thereof, or to give or withhold consent to any corporate action (whether
upon any recapitalization, issuance of stock, reclassification of stock, change
of par value, or change of stock to no par value, consolidation, merger,
conveyance, or otherwise) or to receive notice of meetings, or to receive
dividends or subscription rights or otherwise until the Warrant shall have been
exercised as provided herein.

                                       -4-
<Page>

     8.   TRANSFER OF WARRANT.

     (a)  WARRANT REGISTER. The Company will maintain a register (the "WARRANT
REGISTER") containing the names and addresses of the Holder or Holders. Any
Holder of this Warrant or any portion thereof may change his address as shown on
the Warrant Register by written notice to the Company requesting such change.
Any notice or written communication required or permitted to be given to the
Holder may be delivered or given by mail to such Holder as shown on the Warrant
Register and at the address shown on the Warrant Register. Until this Warrant is
transferred on the Warrant Register of the Company, the Company may treat the
Holder as shown on the Warrant Register as the absolute owner of this Warrant
for all purposes, notwithstanding any notice to the contrary.

     (b)  WARRANT AGENT. The Company may, by written notice to the Holder,
appoint an agent for the purpose of maintaining the Warrant Register referred to
in Section 8(a) above, issuing the common stock, exchanging this Warrant,
replacing this Warrant, or any or all of the foregoing. Thereafter, any such
registration, issuance, exchange, or replacement, as the case may be, shall be
made at the office of such agent.

     (c)  TRANSFERABILITY AND NONNEGOTIABILITY OF WARRANT. This Warrant may not
be transferred or assigned in whole or in part without compliance with all
applicable federal and state securities laws by the transferor and the
transferee (including the delivery of investment representation letters and
legal opinions reasonably satisfactory to the Company, if such are requested by
the Company). Notwithstanding the foregoing, no investment representation letter
or opinion of counsel shall be required for any transfer of this Warrant (or any
portion thereof) or any shares of common stock issued upon exercise hereof (i)
in compliance with Rule 144 or Rule 144A of the Act, or (ii) by gift, will or
intestate succession by the Holder to his or her spouse or lineal descendants or
ancestors or any trust for any of the foregoing; provided that in each of the
foregoing cases the transferee agrees in writing to be subject to the terms of
this Section 8(c). In addition, if the holder of the Warrant (or any portion
thereof) or any common stock issued upon exercise hereof delivers to the Company
an unqualified opinion of counsel that no subsequent transfer of such Warrant or
common stock shall require registration under the Act, the Company shall, upon
such contemplated transfer, promptly deliver new documents/certificates for such
Warrant or common stock that do not bear the legend set forth in Section
8(e)(ii) below. Subject to the provisions of this Warrant with respect to
compliance with the Securities Act of 1933, as amended (the "ACT"), title to
this Warrant may be transferred by endorsement (by the Holder executing the
Assignment Form attached hereto as Exhibit B) and delivery in the same manner as
a negotiable instrument transferable by endorsement and delivery.

     (d)  EXCHANGE OF WARRANT UPON A TRANSFER. On surrender of this Warrant for
exchange, properly endorsed on the Assignment Form and subject to the provisions
of this Warrant with respect to compliance with the Act and with the limitations
on assignments and transfers and contained in this Section 8, the Company shall
issue to or on the order of the Holder a new warrant or warrants of like tenor,
in the name of the Holder or as the Holder (on payment by the Holder of any
applicable transfer taxes) may direct, for the number of shares issuable upon
exercise hereof.

                                       -5-
<Page>

     (e)  COMPLIANCE WITH SECURITIES LAWS.

          (i)   The Holder of this Warrant represents and warrants to the
     Company that it is an accredited investor under the Act. The Holder
     represents and warrants to the Company that it has all of the information
     necessary for it to evaluate an investment in the Company's securities.

          (ii)  The Holder of this Warrant, by acceptance hereof, acknowledges
     that this Warrant and the shares of common stock to be issued upon exercise
     hereof are being acquired solely for the Holder's own account and not as a
     nominee for any other party, and for investment, and that the Holder will
     not offer, sell or otherwise dispose of this Warrant or any shares of
     common stock to be issued upon exercise hereof except under circumstances
     that will not result in a violation of the Act or any applicable state
     securities laws. Upon the exercise of this Warrant, the Holder shall, if
     requested by the Company, confirm in writing, in a form satisfactory to the
     Company, that the shares of common stock so purchased are being acquired
     solely for the Holder's own account and not as a nominee for any other
     party, for investment, and not with a view toward distribution or resale.

          (iii) This Warrant and all shares of common stock issued upon exercise
     hereof shall be stamped or imprinted with a legend in substantially the
     following form (in addition to any legend required by state securities
     laws):

          "NEITHER THIS WARRANT NOR THE SHARES OF STOCK ISSUABLE UPON EXERCISE
          HEREOF, HAVE BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS
          AMENDED. NO SALE, TRANSFER OR OTHER DISPOSITION OF THIS WARRANT OR
          SAID SHARES MAY BE EFFECTED WITHOUT (i) AN EFFECTIVE REGISTRATION
          STATEMENT RELATED THERETO, (ii) AN OPINION OF COUNSEL FOR THE HOLDER,
          REASONABLY SATISFACTORY OR (iii) RECEIPT OF A NO-ACTION LETTER FROM
          THE SECURITIES AND EXCHANGE COMMISSION TO THE EFFECT THAT REGISTRATION
          UNDER THE ACT IS NOT REQUIRED."

          (iv)  The Company agrees to remove promptly, upon the request of the
     holder of this Warrant and Securities issuable upon exercise of the
     Warrant, the legend set forth in Section 8(e)(ii) above from the
     documents/certificates for such securities upon full compliance with this
     Agreement and Rules 144 and 144A.

     9.   RESERVATION OF STOCK. The Company covenants that, the Company will
reserve from its authorized and unissued common stock a sufficient number of
shares to provide for the issuance of common stock upon the exercise of this
Warrant (including any adjustment in the number of Shares pursuant to Section
2(a)). The Company further covenants that all shares that may be issued upon the
exercise of rights represented by this Warrant and payment of the Exercise
Price, all as set forth herein, will be free from all taxes, liens and charges
in respect of the issue thereof (other than taxes in respect of any transfer
occurring contemporaneously or

                                       -6-
<Page>

otherwise specified herein). The Company agrees that its issuance of this
Warrant shall constitute full authority to its officers who are charged with the
duty of executing stock certificates to execute and issue the necessary
certificates for shares of common stock upon the exercise of this Warrant.

     10.  COMPANY REGISTRATION.

     (a)  If (but without the obligation to do so) the Company proposes to
register any of its Common Stock under the Act in connection with the public
offering of such securities solely for cash (other than a registration relating
solely of the sale of securities to participants in any Company stock option,
stock purchase or retirement plan), the Company shall, at each such time,
promptly give to Holder written notice of such registration in the form attached
hereto as Exhibit A-2. Upon the written request of Holder given within twenty
(20) days after mailing of such notice by the Company to Holder's latest address
contained in the Warrant Registry, the Company shall, subject to the provisions
of Section 10(b), cause to be registered under the Act all of the Shares that
Holder has requested to be registered.

     (b)  Holder shall only be able to participate in such registration if it
accepts the terms and conditions of such underwriting as agreed upon between the
Company and its underwriters and Holder agrees that it will abide by the
determination of the underwriters as to the quantity of Holder's Shares to be
offered in the underwriting so as not to jeopardize the success of the offering
by the Company. If the underwriters determine that not all of the Shares will be
included in an offering, Holder may request inclusion in the next public
offering of the Company's Common Stock pursuant to the provisions of Section
10(a).

     11.  EXPENSES OF REGISTRATION. All Registration Expenses (as defined
herein) incurred in connection with any registration, qualification or
compliance pursuant to Section 10 hereof and reasonable fees of one counsel for
Holder shall be borne by the Company. All Selling Expenses (as defined herein)
relating to securities so registered shall be borne by the holders of such
securities PRO RATA on the basis of the number of shares of securities so
registered on their behalf. "REGISTRATION EXPENSES" shall mean all expenses
incurred in effecting any registration pursuant to this Warrant, including,
without limitation, all registration, qualification, and filing fees, printing
expenses, escrow fees, fees and disbursements of counsel for the Company, fees
and disbursements of one special counsel for the selling stockholders, blue sky
fees and expenses, accounting fees and expenses of any regular or special audits
incident to or required by any such registration, but shall not include Selling
Expenses and fees and disbursements of additional counsel for the stockholders.
Registration Expenses do not include the compensation of regular employees of
the Company, which shall be paid in any event by the Company. "SELLING EXPENSES"
shall mean all underwriting discounts and selling commissions applicable to the
sale of Shares and fees and disbursements of counsel for any Holder (other than
the fees and disbursements of counsel included in Registration Expenses).

     12.  AMENDMENTS. This Warrant and any term hereof may be changed, waived,
discharged or terminated only by an instrument in writing signed by the party
against which enforcement of such change, waiver, discharge or termination is
sought.

                                       -7-
<Page>

     13.  MISCELLANEOUS.

     (a)  GOVERNING LAW. This Warrant shall constitute a contract under the laws
of the State of California and for all purposes shall be construed in accordance
with and governed by the laws of said state, without regard to the conflicts of
law provisions thereof.

     (b)  ATTORNEYS' FEES; LITIGATION EXPENSES. In the event of a dispute with
regard to the interpretation of this Warrant, the prevailing party may collect
the cost of attorney's fees, litigation expenses or such other expenses as may
be incurred in the enforcement of the prevailing party's rights hereunder.

     (c)  TRANSFER RESTRICTIONS. The rights to cause the Company to register
securities granted to a Holder by the Company under Section 10 may be
transferred or assigned by Holder only to a transferee or assignee of not less
than 25,000 Shares, provided that the Company is given written notice at the
time of or within a reasonable time after such transfer or assignment, stating
the name and address of the transferee or assignee and identifying the
securities with respect to which such registration rights are being transferred
or assigned, and, provided further, that the transferee or assignee of such
rights assumes the obligations of such Holder under this Warrant.

     (d)  EXPIRATION DATE. This Warrant shall be exercisable as provided for
herein, except that in the event that the expiration date of this Warrant shall
fall on a Saturday, Sunday or United States federally recognized Holiday, this
expiration date for this Warrant shall be extended to 5:00 p.m. Pacific standard
time on the business day following such Saturday, Sunday or recognized Holiday.

     IN WITNESS WHEREOF, the Company has caused this Warrant to be executed by
its one of its officers thereunto duly authorized.

     Dated: April 12, 2002

                                           NANOGEN, INC., a Delaware corporation

                                           By /s/ V. RANDY WHITE
                                              ------------------
                                              V. Randy White
                                              Chief Executive Officer

                                       -8-
<Page>

                                   EXHIBIT A-1
                               NOTICE OF EXERCISE

To:  Nanogen, Inc.                                            Date: ____________
     10398 Pacific Center Court
     San Diego, CA  92121
     Attn:  Vice President, Legal Affairs

Dear Sir:

     (1)  The undersigned hereby elects to purchase shares of common stock of
Nanogen, Inc. (the "COMPANY") either (check box):

                pursuant to the terms of Section 2(a) of the attached Warrant,
          and tenders herewith payment of the purchase price for such shares in
          full or

                pursuant to the net issue provisions of Section 2(b) of the
          Warrant and surrenders the right to purchase _______ shares of Common
          Stock pursuant to the Warrant.

     (2)  In exercising this Warrant, the undersigned hereby confirms and
acknowledges that the shares of common stock to be issued upon conversion
thereof are being acquired solely for the account of the undersigned and not as
a nominee for any other party, or for investment, and that the undersigned will
not offer, sell or otherwise dispose of any such shares of common stock except
under circumstances that will not result in a violation of the Securities Act of
1933, as amended, or any applicable state securities laws.

     (3)  Please issue a certificate or certificates representing said shares of
common stock in the name of the undersigned or in such other name as is
specified below:

                                        ----------------------------------------
                                        (Name)

                                       -9-
<Page>

     (4)  Please issue a new Warrant for the unexercised portion of the attached
Warrant in the name of the undersigned or in such other name as is specified
below:

                                        ----------------------------------------
                                        (Name)

                                        ----------------------------------------
                                        Signature

                                        Address:
                                                 -------------------------------

                                                 -------------------------------

                                      -10-
<Page>

                                   EXHIBIT A-2
                               NOTICE OF EXERCISE
                           (PURSUANT TO REGISTRATION)

To:  Nanogen, Inc.                                              Date: __________
     10398 Pacific Center Court
     San Diego, CA  92121
     Attn:  Vice President, Legal Affairs

Dear Sir:

     (1)  Contingent upon and effective immediately prior to the closing (the
"CLOSING") of the Company's public offering contemplated by the Registration
Statement on Form S-_, filed with the Securities and Exchange Commission on
__________________________, 20__, the undersigned hereby elects to purchase
____________________ shares of Common Stock of the Company (or such lesser
number of shares as may be sold on behalf of the undersigned at the Closing)
pursuant to the terms of the attached Warrant.

     (2)  Please deliver to the custodian for the selling stockholders a stock
certificate representing such ________ shares.

     (3)  The undersigned has instructed the custodian for the selling
stockholders to deliver to the Company $__________________ or, if less, the net
proceeds due the undersigned from the sale of shares in the aforesaid public
offering. If such net proceeds are less than the purchase price for such shares,
the undersigned agrees to deliver the difference to the Company prior to the
Closing.

     (4)  Please issue a certificate or certificates representing said shares of
common stock in the name of the undersigned or in such other name as is
specified below:

                                        ----------------------------------------
                                        (Name)

                                      -11-
<Page>

     (5)  Please issue a new Warrant for the unexercised portion of the attached
Warrant in the name of the undersigned or in such other name as is specified
below:

                                        ----------------------------------------
                                        (Name)

                                        ----------------------------------------
                                        Signature

                                        Address:
                                                 -------------------------------

                                                 -------------------------------

                                      -12-
<Page>

                                    EXHIBIT B
                                 ASSIGNMENT FORM

To:  Nanogen, Inc.                                              Date: __________
     10398 Pacific Center Court
     San Diego, CA  92121
     Attn:  Vice President, Legal Affairs

Dear Sir:

     FOR VALUE RECEIVED, the undersigned registered owner of this Warrant hereby
sells, assigns and transfers unto the Assignee named below all of the rights of
the undersigned under the within Warrant, with respect to the number of shares
of common stock set forth below:

Name of Assignee                 Address                      No. of Shares
------------------------------   ---------------------------  ------------------

and does hereby irrevocably constitute and appoint the Vice President, Legal
Affairs of Nanogen, Inc. (the "COMPANY") to make such transfer on the books of
the Company, maintained for the purpose, with full power of substitution in the
premises.

     The undersigned also represents that, by assignment hereof, the Assignee
acknowledges that this Warrant and the shares of stock to be issued upon
exercise hereof or conversion thereof are being acquired for investment and that
the Assignee will not offer, sell or otherwise dispose of this Warrant or any
shares of stock to be issued upon exercise hereof or conversion thereof except
under circumstances which will not result in a violation of the Securities Act
of 1933, as amended, or any applicable state securities laws. Further, the
Assignee has acknowledged that upon exercise of this Warrant, the Assignee
shall, if requested by the Company, confirm in writing, in a form satisfactory
to the Company, that the shares of stock so purchased are being acquired for
investment and not with a view toward distribution or resale.

                                        ----------------------------------------
                                        Signature (of Holder)

                                        Address:
                                                 -------------------------------

                                                 -------------------------------

                                      -13-

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