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Exhibit 10.1

SECOND AMENDMENT TO EMPLOYMENT AGREEMENT

    This Second Amendment to Employment Agreement ("Amendment"), effective as of
July 1, 2001, is made by and between NANOGEN, INC., a Delaware corporation (the
"Company"), and MICHAEL D. MOORE (the "Executive").

RECITALS

    WHEREAS, the Company and Executive have entered into an Employment Agreement
dated December 6, 1999, superceded by an Employment Agreement dated June 15,
2000 and a First Amendment to Employment Agreement dated July 28, 2000
(collectively the "Employment Agreement"); and

    WHEREAS, the Company and Executive wish to amend the Employment Agreement as
described herein.

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

TERMS

1. Title/Responsibilities.  In Article II, Section A (Title/Responsibilities) of
the Employment Agreement, Executive's title is stated to be "Senior Vice
President and General Manager". The title and position of "Senior Vice President
and General Manager" is hereby deleted from the Employment Agreement, and the
title and position of "Senior Vice President, Operations" is substituted.

2.Full Time Attention.  Article II, Section B (Full Time Attention) of the
Employment Agreement requires Executive to "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". This language is hereby deleted, and the following language is
substituted: "Executive shall devote his best efforts and his 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 while working three full
(3) days per week at the Nanogen San Diego office and one full (1) day per week
from his Bay Area residence".

3.Base Salary.  Article III, Section A (Base Salary) of the Employment Agreement
sets Executive's base salary at $250,000 per year. This language is hereby
deleted, and the annual Base Salary is hereby set at the rate of one hundred
fifty thousand dollars ($150,000).

4.Stock Options.  Article IV, Section E (Stock Options) of the Employment
Agreement provides for certain vesting schedules for stock options granted to
Executive at various times. Effective July 1, 2001, Executive's stock options
will vest at eighty percent (80%) of his current vesting schedule, as set forth
in Exhibit A attached hereto and incorporated herein. Should additional stock
options be granted to Executive in the future, they also will vest at eighty
percent (80%) of the vesting schedule provided to full time employees at
Executive's level.

5.No Constructive Termination.  Executive acknowledges that the foregoing
amendments to the Employment Agreement do not constitute Constructive
Termination of Executive's employment as that term is defined in Article VI,
Section E (Constructive Termination) of the Employment Agreement.

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6.Remainder of Agreement.  The other terms and conditions contained in the
Employment Agreement shall remain in effect pursuant to the Employment Agreement
and such terms and conditions, where applicable, shall also govern this
Amendment.

7.Governing Law.  This Amendment shall be construed in accordance with the laws
of the State of California, notwithstanding its conflicts of law provisions.

8.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 Amendment, and has been advised to do so by the Company,
and (b) that he has read and understands this Amendment, is fully aware of its
legal effect, and has entered into it freely based on his own judgment.

9.Counterparts.  This Amendment may be executed in one or more counterparts, all
of which taken together constituted one and the same agreement.

    NANOGEN, INC.
 
 
By:
 
/s/ V. RANDY WHITE   
6/21/01        

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        V. Randy White
Chief Executive Officer Date
 
 
EXECUTIVE
 
 
By:
 
/s/ MICHAEL D. MOORE   
7/01/01        

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        Michael D. Moore Date

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Exhibit 10.1

SECOND AMENDMENT TO EMPLOYMENT AGREEMENT