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Employment Agreement - Nanogen Inc. and Steven J. Naber

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                              [NANOGEN LETTERHEAD]

September 24, 1997

Steven J. Naber
11 Fair Elms
Laguna Niguel, CA 92677

Dear Steve:

Nanogen Incorporated ("Nanogen") is pleased to offer you the position of Vice
President Finance/Chief Financial Officer, with Nanogen Incorporated and the
following terms encompass our offer. The effective date of this position will be
as soon as possible, but hopefully not later than October 20, 1997. If you
accept this offer, you will be an exempt employee reporting to me, Nanogen's

You will be located in our San Diego office, and as Vice President Finance/CFO,
will be responsible for directing financial operations for Nanogen, including
our initial stock offering and related activities. You will be expected to
devote your full-time efforts to these responsibilities, and you will be
compensated at an annual base rate of $165,000 per annum payable in equal,
semi-monthly increments.

As a Vice President, you will be a participant in Nanogen's Executive Incentive
Compensation Plan. As part of this plan, you will be grandfathered into the 1997
incentive plan and eligible for a bonus of up to $20,000 for 1997, and $40,000
for 1998. All bonuses are based on annual milestones which would be mutually
agreed upon between you and me, and subject to Board of Directors' approval.

Upon your acceptance of this proposal, you will be entitled to purchase 150,000
shares of Nanogen common stock at fair market value, as determined by Nanogen's
Board, upon the terms contained in the Company's Stock Purchase Agreement which
includes a four-year vesting/repurchasing provision.

You will be eligible to participate in all Company-sponsored benefits upon your
date of hire. At present, these include full medical, dental and vision
insurance coverage for yourself, with the option to include your family with a
minimal contribution. In addition, you will be eligible to participate in our
life and long-term disability insurance as well as our 401(k) plans
(non-employer contributing) as well as our 125 Flexible Benefits Program. A
benefits summary is included for your review.

<PAGE>   2

Steven J. Naber
September 24, 1997
Page 2

Should you choose to relocate your household from Orange County to San Diego
during your first nine months of employment, you will be eligible for relocation
benefits consistent with your employment level at Nanogen. A copy of Nanogen's
1997 Executive Relocation Guidelines are provided to you herewith. In addition
to the relocation benefits contained in the guidelines, Nanogen is willing to
offer to cover the cost of temporary housing (to be arranged by Nanogen) during
your first nine months of employment, up to a monthly cap of $3,000.

The Company also agrees to provide you with six months of severance pay, should
your employment be terminated without cause: a) during your first year of
employment, or b) before the time in which shares of Nanogen common stock have
been sold in an initial public offering, if this has not taken place during your
first year of employment. For the purpose of this letter, the phrase
"termination without cause" shall mean a termination of your employment by
Nanogen for any reason other than: 1) the repeated and willful failure by you to
perform your reasonably assigned duties on behalf of Nanogen; 2) the repeated
gross negligence by you in carrying out your duties; 3) illegal conduct by you
in carrying out your duties; 4) the repeated refusal by you to comply with the
reasonable and lawful instructions of the Board; or 5) repeated and willful
actions by you contrary to Nanogen's best interests.

Employment with Nanogen will not be for a specific term and can be terminated by
you or by the Company at any time for any reason, with or without cause and with
or without notice. Any contrary representations, agreements, or promises of any
kind, whether written, oral, expressed or implied which may have been made or
which may be made to you are/will be superseded by this offer. We request that
all Nanogen employees, to the extent possible, give advance notice if they
intend to resign. If you accept the offer, the terms described in this letter
will be the terms of your employment. Any additions or modifications of these
terms must be in writing and signed by you and Nanogen's Chief Executive

As an obligation consistent with the offer of employment, you will be required
to sign the enclosed Blood Consent Form, and the Proprietary Information and
Inventions Agreement; and on your first day of employment, to provide the
Company with the legally required proof of your identity and authorization to
work in the United States.

Assuming this letter is acceptable to you, please sign a copy and return it to
me. This offer will terminate unless accepted by October 6, 1997. We are very
excited that you

<PAGE>   3

Steven J. Naber
September 24, 1997
Page 3

will be joining Nanogen.  Myself, Tina, our Board Members and employees look
forward to announcing your appointment.

Sincerely yours,


Howard C. Birndorf


I accept this offer under the terms and conditions set forth in this letter.

/s/ STEVEN J. NABER                               9-26-97
---------------------------------                 ---------------------------
Steven J. Naber                                   Date