NANOGEN INC
EXHIBIT 10.1
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<DESCRIPTION>EXHIBIT 10.1
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NAME="kc1982_exhibit_10.1"> </A>
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<BR></FONT><FONT SIZE=2><B>Exhibit 10.1    <BR>  </B></FONT></P>

<P ALIGN="CENTER"><FONT SIZE=2><A
NAME="kc1982_second_amendment_to_employment_agreement"> </A>
<A NAME="toc_kc1982_2"> </A>
<BR></FONT><FONT SIZE=2><I>SECOND AMENDMENT TO EMPLOYMENT AGREEMENT    <BR>  </I></FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;This Second Amendment to Employment Agreement ("Amendment"), effective as of July&nbsp;1, 2001, is made by and between NANOGEN,&nbsp;INC., a Delaware
corporation (the "Company"), and MICHAEL D. MOORE (the "Executive"). </FONT></P>

<P ALIGN="CENTER"><FONT SIZE=2><I>RECITALS  </I></FONT></P>


<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;WHEREAS, the Company and Executive have entered into an Employment Agreement dated December&nbsp;6, 1999, superceded by an Employment Agreement dated
June&nbsp;15, 2000 and a First Amendment to Employment Agreement dated July&nbsp;28, 2000 (collectively the "Employment Agreement"); and </FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;WHEREAS,
the Company and Executive wish to amend the Employment Agreement as described herein. </FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;NOW,
THEREFORE, the Company and Executive, in consideration of the Executive's continued employment with the Company, agree as follows: </FONT></P>

<P ALIGN="CENTER"><FONT SIZE=2><I>TERMS  </I></FONT></P>

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<DT><FONT SIZE=2><I>1.</I></FONT></DT><DD><FONT SIZE=2><I> Title/Responsibilities</I></FONT><FONT SIZE=2>.&nbsp;&nbsp;In Article&nbsp;II, Section&nbsp;A (</FONT><FONT SIZE=2><I>Title/Responsibilities</I></FONT><FONT SIZE=2>) 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.
<BR><BR></FONT></DD><DT><FONT SIZE=2>2.</FONT></DT><DD><FONT SIZE=2><I>Full Time Attention</I></FONT><FONT SIZE=2>.&nbsp;&nbsp;Article&nbsp;II, Section&nbsp;B (</FONT><FONT SIZE=2><I>Full Time
Attention</I></FONT><FONT SIZE=2>) 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)&nbsp;days per week at the Nanogen San Diego office and one full (1)&nbsp;day per week from his Bay Area residence".
<BR><BR></FONT></DD><DT><FONT SIZE=2>3.</FONT></DT><DD><FONT SIZE=2><I>Base Salary</I></FONT><FONT SIZE=2>.&nbsp;&nbsp;Article&nbsp;III, Section&nbsp;A (</FONT><FONT SIZE=2><I>Base Salary</I></FONT><FONT SIZE=2>) 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).
<BR><BR></FONT></DD><DT><FONT SIZE=2>4.</FONT></DT><DD><FONT SIZE=2><I>Stock Options</I></FONT><FONT SIZE=2>.&nbsp;&nbsp;Article&nbsp;IV, Section&nbsp;E (</FONT><FONT SIZE=2><I>Stock Options</I></FONT><FONT SIZE=2>) of
the Employment Agreement provides for certain vesting schedules for stock options granted to Executive at various times. Effective July&nbsp;1, 2001, Executive's stock options will vest at eighty
percent (80%) of his current vesting schedule, as set forth in Exhibit&nbsp;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.
<BR><BR></FONT></DD><DT><FONT SIZE=2>5.</FONT></DT><DD><FONT SIZE=2><I>No Constructive Termination</I></FONT><FONT SIZE=2>.&nbsp;&nbsp;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&nbsp;VI, Section&nbsp;E (</FONT><FONT SIZE=2><I>Constructive Termination</I></FONT><FONT SIZE=2>)
of the Employment Agreement. </FONT></DD></DL>
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<DT><FONT SIZE=2>6.</FONT></DT><DD><FONT SIZE=2><I>Remainder of Agreement</I></FONT><FONT SIZE=2>.&nbsp;&nbsp;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.
<BR><BR></FONT></DD><DT><FONT SIZE=2>7.</FONT></DT><DD><FONT SIZE=2><I>Governing Law</I></FONT><FONT SIZE=2>.&nbsp;&nbsp;This Amendment shall be construed in accordance with the laws of the State of California,
notwithstanding its conflicts of law provisions.
<BR><BR></FONT></DD><DT><FONT SIZE=2>8.</FONT></DT><DD><FONT SIZE=2><I>Executive Acknowledgment</I></FONT><FONT SIZE=2>.&nbsp;&nbsp;Executive acknowledges (a)&nbsp;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)&nbsp;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.
<BR><BR></FONT></DD><DT><FONT SIZE=2>9.</FONT></DT><DD><FONT SIZE=2><I>Counterparts</I></FONT><FONT SIZE=2>.&nbsp;&nbsp;This Amendment may be executed in one or more counterparts, all of which taken together constituted one
and the same agreement. </FONT></DD></DL>
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<TD COLSPAN=4><FONT SIZE=2>NANOGEN,&nbsp;INC.</FONT></TD>
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/s/&nbsp;</FONT><FONT SIZE=2>V. RANDY WHITE</FONT><FONT SIZE=2>&nbsp;&nbsp;&nbsp;</FONT></TD>
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6/21/01</FONT></TD>
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<TD WIDTH="41%"><FONT SIZE=2>V. Randy White<BR></FONT> <FONT SIZE=2><I>Chief Executive Officer</I></FONT></TD>
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EXECUTIVE</FONT></TD>
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/s/&nbsp;</FONT><FONT SIZE=2>MICHAEL D. MOORE</FONT><FONT SIZE=2>&nbsp;&nbsp;&nbsp;</FONT></TD>
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7/01/01</FONT></TD>
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<TD WIDTH="41%"><FONT SIZE=2>Michael D. Moore</FONT></TD>
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