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<P ALIGN="CENTER"><FONT SIZE=2><B>As filed with the Securities and Exchange Commission on June&nbsp;20, 2001  </B></FONT></P>

<P ALIGN="RIGHT"><FONT SIZE=2><B> Registration No. 333-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</B></FONT></P>

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<P ALIGN="CENTER"><FONT SIZE=5><B>SECURITIES AND EXCHANGE COMMISSION<BR>  </B></FONT><FONT SIZE=2><B>Washington, D.C. 20549  </B></FONT></P>

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<P ALIGN="CENTER"><FONT SIZE=5><B>FORM S-8<BR>  </B></FONT><FONT SIZE=2><B>REGISTRATION STATEMENT<BR>
UNDER<BR>
THE SECURITIES ACT OF 1933  </B></FONT></P>

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<P ALIGN="CENTER"><FONT SIZE=5><B>NANOGEN, INC.<BR>  </B></FONT><FONT SIZE=2>(Exact name of Registrant as specified in its charter) </FONT></P>

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<TD WIDTH="33%" ALIGN="CENTER"><FONT SIZE=2><B>Delaware</B></FONT><FONT SIZE=2><BR>
(State of incorporation)</FONT></TD>
<TD WIDTH="33%" ALIGN="CENTER"><FONT SIZE=2><B>10398 Pacific Center Court,<BR>
San Diego, CA 92121</B></FONT></TD>
<TD WIDTH="33%" ALIGN="CENTER"><FONT SIZE=2><B>33-0489621</B></FONT><FONT SIZE=2><BR>
(I.R.S. Employer Identification Number)</FONT></TD>
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<P ALIGN="CENTER"><FONT SIZE=2>(Address,
including zip code, of Registrant's principal executive offices) </FONT></P>

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<P ALIGN="CENTER"><FONT SIZE=2>Nanogen,
Inc. 1997 Stock Incentive Plan, as amended </FONT></P>

<P ALIGN="CENTER"><FONT SIZE=2>(Full
title of the plan) </FONT></P>

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<P ALIGN="CENTER"><FONT SIZE=2><B>Vera P. Pardee, Esq.<BR>
Vice President, General<BR>
Counsel and Secretary<BR>
10398 Pacific Center Court,<BR>
San Diego, CA 92121  </B></FONT></P>

<P ALIGN="CENTER"><FONT SIZE=2>(Name, address, including zip code, and telephone number, including area code, of agent for service) </FONT></P>

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<P ALIGN="CENTER"><FONT SIZE=2><I>Copy to:  </I></FONT></P>

<P ALIGN="CENTER"><FONT SIZE=2>John L. Donahue, Esq.<BR>
Wilson Sonsini Goodrich &amp; Rosati<BR>
Professional Corporation<BR>
650 Page Mill Road<BR>
Palo Alto, CA 94304<BR>
(650) 493-9300 </FONT></P>

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<P ALIGN="CENTER"><FONT SIZE=2><B>CALCULATION OF REGISTRATION FEE  </B></FONT></P>

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<TD WIDTH="36%" ALIGN="CENTER" VALIGN="BOTTOM"><FONT SIZE=1><B>Title of Securities to<BR>
be Registered</B></FONT></TD>
<TD WIDTH="1%" VALIGN="BOTTOM"><FONT SIZE=1>&nbsp;</FONT></TD>
<TD WIDTH="15%" ALIGN="CENTER" VALIGN="BOTTOM"><FONT SIZE=1><B>Amount<BR>
to be<BR>
Registered(1)</B></FONT></TD>
<TD WIDTH="1%" VALIGN="BOTTOM"><FONT SIZE=1>&nbsp;</FONT></TD>
<TD WIDTH="15%" ALIGN="CENTER" VALIGN="BOTTOM"><FONT SIZE=1><B>Proposed<BR>
Maximum<BR>
Offering Price Per<BR>
Share(2)</B></FONT></TD>
<TD WIDTH="1%" VALIGN="BOTTOM"><FONT SIZE=1>&nbsp;</FONT></TD>
<TD WIDTH="15%" ALIGN="CENTER" VALIGN="BOTTOM"><FONT SIZE=1><B>Proposed<BR>
Maximum<BR>
Aggregate<BR>
Offering Price</B></FONT></TD>
<TD WIDTH="1%" VALIGN="BOTTOM"><FONT SIZE=1>&nbsp;</FONT></TD>
<TD WIDTH="15%" ALIGN="CENTER" VALIGN="BOTTOM"><FONT SIZE=1><B>Amount of<BR>
Registration<BR>
Fee</B></FONT></TD>
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<TD COLSPAN=9 VALIGN="BOTTOM"><HR NOSHADE></TD>
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<TD WIDTH="36%"><FONT SIZE=2>Common Stock, par value $0.001, including related Series&nbsp;A Participating Preferred Stock Purchase Rights</FONT></TD>
<TD WIDTH="1%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="15%" ALIGN="CENTER"><FONT SIZE=2>1,500,000</FONT></TD>
<TD WIDTH="1%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="15%" ALIGN="CENTER"><FONT SIZE=2>$8.61</FONT></TD>
<TD WIDTH="1%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="15%" ALIGN="CENTER"><FONT SIZE=2>$12,915,000</FONT></TD>
<TD WIDTH="1%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="15%" ALIGN="CENTER"><FONT SIZE=2>$3,229</FONT></TD>
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<DL compact>
<DT><FONT SIZE=2>(1)</FONT></DT><DD><FONT SIZE=2>This
Registration Statement shall also cover any additional shares of Common Stock which become issuable by reason of any stock dividend, stock split, recapitalization or other
similar transaction effected without the receipt of consideration which results in an increase in the number of the outstanding shares of Common Stock.
<BR><BR></FONT></DD><DT><FONT SIZE=2>(2)</FONT></DT><DD><FONT SIZE=2>Estimated
pursuant to Rule 457(h) under the Securities Act of 1933, as amended (the "Securities Act") solely for the purpose of calculating the registration fee. </FONT></DD></DL>
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<BR></FONT><FONT SIZE=2><B>INFORMATION REQUIRED PURSUANT TO GENERAL INSTRUCTION E TO FORM&nbsp;S-8    <BR>  </B></FONT></P>

<P><FONT SIZE=2><B>General Instruction E Information  </B></FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;This Registration Statement is being filed for the purpose of increasing the number of securities of the same class as other securities for which Registration
Statements of the Registrant on Form&nbsp;S-8 relating to the same employee benefit plan are effective. Registrant's Form&nbsp;S-8 Registration Statements filed with the Securities and Exchange
Commission on April 17, 1998 (No.&nbsp;333-50381), July&nbsp;29, 1999 (File No.&nbsp;333-83993) and June&nbsp;15, 2000 (File&nbsp;No. 333-39376) are hereby incorporated by reference. </FONT></P>

<P ALIGN="CENTER"><FONT SIZE=2><A
NAME="ja1530_part_ii_information_req__ja102467"> </A>
<A NAME="toc_ja1530_2"> </A>
<BR></FONT><FONT SIZE=2><B>PART II<BR>  <BR>    INFORMATION REQUIRED IN THE REGISTRATION STATEMENT    <BR>  </B></FONT></P>

<P><FONT SIZE=2><B>Item 3.&nbsp;&nbsp;Incorporation of Documents by Reference  </B></FONT></P>


<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;There are hereby incorporated by reference into this Registration Statement and into the Prospectuses relating to this Registration Statement pursuant to
Rule&nbsp;428 the following documents and information previously filed with the Securities and Exchange Commission: </FONT></P>

<UL>
<DL compact>
<DT><FONT SIZE=2>1</FONT></DT><DD><FONT SIZE=2>The
Registrant's Annual Report on Form 10-K for the year ended December&nbsp;31, 2000, filed pursuant to Section&nbsp;13(a) of the Securities Exchange Act of 1934, as amended
('the Exchange Act') (File No.&nbsp;0-23541);
<BR><BR></FONT></DD><DT><FONT SIZE=2>2.</FONT></DT><DD><FONT SIZE=2>The
Registrant's Quarterly Report on Form&nbsp;10-Q for the quarter ended March&nbsp;31, 2001;
<BR><BR></FONT></DD><DT><FONT SIZE=2>3.</FONT></DT><DD><FONT SIZE=2>The
description of Registrant's Common Stock contained in Registrant's Registration Statement on Form&nbsp;8-A filed with the Commission on April&nbsp;7, 1998; and
<BR><BR></FONT></DD><DT><FONT SIZE=2>4.</FONT></DT><DD><FONT SIZE=2>The
description of the Preferred Stock Purchase Rights for Series&nbsp;A Participating Preferred Stock, par value $.001 per share of the Registrant contained in Registrant's
Registration Statement on Form&nbsp;8-A filed November&nbsp;24, 1998. </FONT></DD></DL>
</UL>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;All
documents filed by the Registrant pursuant to Sections 13(a), 13(c), 14 and 15(d) of the Exchange Act after the date hereof, and prior to the filing of a post-effective amendment
which indicates that all securities offered have been sold or which deregisters all securities then remaining unsold, shall be deemed to be incorporated by reference herein and to be part hereof from
the date of filing of such documents. </FONT></P>

<P><FONT SIZE=2><B>Item 8.&nbsp;&nbsp;Exhibits  </B></FONT></P>

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<TH WIDTH="9%" ALIGN="CENTER"><FONT SIZE=1><B>Exhibit No.</B></FONT><HR NOSHADE></TH>
<TH WIDTH="3%"><FONT SIZE=1>&nbsp;</FONT></TH>
<TH WIDTH="89%" ALIGN="LEFT"><FONT SIZE=1><B>Document<BR> </B></FONT><HR NOSHADE></TH>
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<TD WIDTH="9%" ALIGN="RIGHT"><FONT SIZE=2>5.1</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="89%"><FONT SIZE=2>Opinion of Wilson Sonsini Goodrich &amp; Rosati, Professional Corporation ('WSGR').</FONT></TD>
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<TD WIDTH="9%" ALIGN="RIGHT"><FONT SIZE=2>23.1</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="89%"><FONT SIZE=2>Consent of Ernst &amp; Young LLP, Independent Auditors</FONT></TD>
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<TD WIDTH="9%" ALIGN="RIGHT"><FONT SIZE=2>23.2</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="89%"><FONT SIZE=2>Consent of WSGR (contained in Exhibit&nbsp;5.1)</FONT></TD>
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<TD WIDTH="9%" ALIGN="RIGHT"><FONT SIZE=2>24.1</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="89%"><FONT SIZE=2>Power of Attorney (see page&nbsp;4.)</FONT></TD>
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<P><FONT SIZE=2><B>Item 9.&nbsp;&nbsp;Undertakings  </B></FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;(a)&nbsp;The
undersigned Registrant hereby undertakes: </FONT></P>

<UL>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;(1)&nbsp;To
file, during any period in which offers or sales are being made, a post-effective amendment to this Registration Statement to include any material information
with respect to the plan of distribution not previously disclosed in the Registration Statement or any material change to such information in the Registration Statement. </FONT></P>

</UL>
<P ALIGN="CENTER"><FONT SIZE=2>1</FONT></P>

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&nbsp;&nbsp;&nbsp;&nbsp;(2)&nbsp;That, for the purpose of determining any liability under the Securities Act of 1933, as amended (the 'Securities Act'), each such post-effective amendment shall be
deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof. </FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;(3)&nbsp;To
remove from registration by means of a post-effective amendment any of the securities being registered which remain unsold at the termination of the offering. </FONT></P>

</UL>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;(b)&nbsp;The
undersigned Registrant hereby undertakes that, for purposes of determining any liability under the Securities Act, each filing of the Registrant's annual report
pursuant to Section 13(a) or Section 15(d) of the Securities Exchange Act of 1934 that is incorporated by reference in the registration statement shall be deemed to be a new registration statement
relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof. </FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;(c)&nbsp;Insofar
as indemnification for liabilities arising under the Securities Act may be permitted to directors, officers and controlling persons of the Registrant
pursuant to the foregoing provisions, or otherwise, the Registrant has been advised that in the opinion of the Securities and Exchange Commission such indemnification is against public policy as
expressed in the Securities Act and is, therefore, unenforceable. In the event that a claim for indemnification against such liabilities (other than the payment by the Registrant of expenses incurred
or paid by a director, officer or controlling person of the Registrant in the successful defense of any action, suit or proceeding) is asserted by such director, officer or controlling person in
connection with the securities being registered, the Registrant will, unless in the opinion of its counsel the matter has been settled by controlling precedent, submit to a court of appropriate
jurisdiction the question whether such indemnification by it is against public policy as expressed in the Securities Act and will be governed by the final adjudication of such issue. </FONT></P>

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

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<BR></FONT><FONT SIZE=2><B>SIGNATURES    <BR>  </B></FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Act of 1933, the Registrant, Nanogen, Inc., certifies that it has reasonable grounds to believe that it meets
all of the requirements for filing on Form&nbsp;S-8 and has duly caused this Registration Statement on Form&nbsp;S-8 to be signed on its behalf by the undersigned, thereunto duly authorized, in
the city of San Diego, State of California, on the 19th day of June, 2001. </FONT></P>

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<TD WIDTH="47%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD COLSPAN=2><FONT SIZE=2>NANOGEN, INC.</FONT></TD>
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<TD WIDTH="47%"><FONT SIZE=2><BR>
&nbsp;</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="4%"><FONT SIZE=2><BR>
By:</FONT></TD>
<TD WIDTH="46%" ALIGN="CENTER"><FONT SIZE=2><BR>
/s/&nbsp;</FONT><FONT SIZE=2>VANCE RANDY WHITE</FONT><FONT SIZE=2>&nbsp;&nbsp;&nbsp;</FONT><HR NOSHADE><FONT SIZE=2> Vance Randy White<BR></FONT> <FONT SIZE=2><I>Chief Executive Officer</I></FONT></TD>
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<P ALIGN="CENTER"><FONT SIZE=2><A
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<BR></FONT><FONT SIZE=2><B>POWER OF ATTORNEY    <BR>  </B></FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;</FONT><FONT
SIZE=2><B>KNOW ALL PERSONS BY THESE PRESENTS,</B></FONT><FONT SIZE=2> that each person whose signature appears below constitutes and appoints Kiernan T. Gallahue and
Vera P. Pardee and each of them, acting individually, as his attorney-in-fact, with full power of substitution, for him and in any and all capacities, to sign any and all amendments to this
Registration Statement on Form S-8 (including post-effective amendments) and to file the same, with all exhibits thereto and other documents in connection therewith, with the Securities and Exchange
Commission, hereby ratifying and confirming our signatures as they may be signed by our said attorney to any and all amendments to the Registration Statement on Form S-8. </FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;Pursuant
to the requirements of the Securities Act of 1933, this Registration Statement on Form S-8 has been signed by the following persons in the capacities and on the dates
indicated. </FONT></P>

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<TH WIDTH="45%" ALIGN="CENTER"><FONT SIZE=1><B>Signature</B></FONT><HR NOSHADE></TH>
<TH WIDTH="2%"><FONT SIZE=1>&nbsp;</FONT></TH>
<TH WIDTH="33%" ALIGN="CENTER"><FONT SIZE=1><B>Title</B></FONT><HR NOSHADE></TH>
<TH WIDTH="2%"><FONT SIZE=1>&nbsp;</FONT></TH>
<TH WIDTH="18%" ALIGN="CENTER"><FONT SIZE=1><B>Date</B></FONT><HR NOSHADE></TH>
</TR>
<TR VALIGN="BOTTOM">
<TD WIDTH="45%" ALIGN="CENTER" VALIGN="CENTER"><BR><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="33%" VALIGN="CENTER"><FONT SIZE=2><BR>
&nbsp;</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="18%" VALIGN="CENTER"><FONT SIZE=2><BR>
&nbsp;</FONT></TD>
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<TD WIDTH="45%" ALIGN="CENTER" VALIGN="CENTER"><FONT SIZE=2>/s/&nbsp;</FONT><FONT SIZE=2>VANCE RANDY WHITE</FONT><FONT SIZE=2>&nbsp;&nbsp;&nbsp;</FONT><HR NOSHADE><FONT SIZE=2> Vance Randy White</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="33%" VALIGN="CENTER"><FONT SIZE=2>Chief Executive Officer and Director (Principal Executive Officer)</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="18%" ALIGN="CENTER" VALIGN="CENTER"><FONT SIZE=2>June&nbsp;19, 2001</FONT></TD>
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<TD WIDTH="45%" ALIGN="CENTER" VALIGN="CENTER"><FONT SIZE=2><BR>
/s/&nbsp;</FONT><FONT SIZE=2>GERARD A. WILLS</FONT><FONT SIZE=2>&nbsp;&nbsp;&nbsp;</FONT><HR NOSHADE><FONT SIZE=2> Gerard A. Wills</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="33%" VALIGN="CENTER"><FONT SIZE=2><BR>
Vice President, Chief Financial Officer and Treasurer (Principal Financial and Accounting Officer)</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="18%" ALIGN="CENTER" VALIGN="CENTER"><FONT SIZE=2><BR>
June&nbsp;19, 2001</FONT></TD>
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<TD WIDTH="45%" ALIGN="CENTER" VALIGN="CENTER"><FONT SIZE=2><BR>
/s/&nbsp;</FONT><FONT SIZE=2>HOWARD C. BIRNDORF</FONT><FONT SIZE=2>&nbsp;&nbsp;&nbsp;</FONT><HR NOSHADE><FONT SIZE=2> Howard C. Birndorf</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="33%" VALIGN="CENTER"><FONT SIZE=2><BR>
Chairman of the Board of Directors</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="18%" ALIGN="CENTER" VALIGN="CENTER"><FONT SIZE=2><BR>
June&nbsp;19, 2001</FONT></TD>
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<TD WIDTH="45%" ALIGN="CENTER" VALIGN="CENTER"><FONT SIZE=2><BR>
/s/&nbsp;</FONT><FONT SIZE=2>VAL BUONAIUTO</FONT><FONT SIZE=2>&nbsp;&nbsp;&nbsp;</FONT><HR NOSHADE><FONT SIZE=2> Val Buonaiuto</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="33%" VALIGN="CENTER"><FONT SIZE=2><BR>
Director</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="18%" ALIGN="CENTER" VALIGN="CENTER"><FONT SIZE=2><BR>
June&nbsp;19, 2001</FONT></TD>
</TR>
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<TD WIDTH="45%" ALIGN="CENTER" VALIGN="CENTER"><BR><HR NOSHADE><FONT SIZE=2> Cam L. Garner</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="33%" VALIGN="CENTER"><FONT SIZE=2><BR>
Director</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="18%" ALIGN="CENTER" VALIGN="CENTER"><FONT SIZE=2><BR>
June&nbsp;&nbsp;, 2001</FONT></TD>
</TR>
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<TD WIDTH="45%" ALIGN="CENTER" VALIGN="CENTER"><BR><HR NOSHADE><FONT SIZE=2> Regina E. Herzlinger</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="33%" VALIGN="CENTER"><FONT SIZE=2><BR>
Director</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="18%" ALIGN="CENTER" VALIGN="CENTER"><FONT SIZE=2><BR>
June&nbsp;&nbsp;, 2001</FONT></TD>
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<TD WIDTH="45%" ALIGN="CENTER" VALIGN="CENTER"><FONT SIZE=2><BR>
/s/&nbsp;</FONT><FONT SIZE=2>DAVID G. LUDVIGSON</FONT><FONT SIZE=2>&nbsp;&nbsp;&nbsp;</FONT><HR NOSHADE><FONT SIZE=2> David G. Ludvigson</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="33%" VALIGN="CENTER"><FONT SIZE=2><BR>
Director</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="18%" ALIGN="CENTER" VALIGN="CENTER"><FONT SIZE=2><BR>
June&nbsp;19, 2001</FONT></TD>
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<TD WIDTH="45%" ALIGN="CENTER" VALIGN="CENTER"><BR><HR NOSHADE><FONT SIZE=2> Stelios B. Papadopoulos</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="33%" VALIGN="CENTER"><FONT SIZE=2><BR>
Director</FONT></TD>
<TD WIDTH="2%" VALIGN="CENTER"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="18%" ALIGN="CENTER" VALIGN="CENTER"><FONT SIZE=2><BR>
June&nbsp;&nbsp;, 2001</FONT></TD>
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<P ALIGN="CENTER"><FONT SIZE=2>3</FONT></P>

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<BR></FONT><FONT SIZE=2><B>INDEX TO EXHIBITS    <BR>  </B></FONT></P>

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<TH WIDTH="9%" ALIGN="CENTER"><FONT SIZE=1><B>Exhibit No.</B></FONT><HR NOSHADE></TH>
<TH WIDTH="3%"><FONT SIZE=1>&nbsp;</FONT></TH>
<TH WIDTH="89%" ALIGN="LEFT"><FONT SIZE=1><B>Document<BR> </B></FONT><HR NOSHADE></TH>
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<TD WIDTH="9%" ALIGN="RIGHT"><FONT SIZE=2>5.1</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="89%"><FONT SIZE=2>Opinion of Wilson Sonsini Goodrich &amp; Rosati, Professional Corporation ('WSGR')</FONT></TD>
</TR>
<TR BGCOLOR="White" VALIGN="TOP">
<TD WIDTH="9%" ALIGN="RIGHT"><FONT SIZE=2>23.1</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="89%"><FONT SIZE=2>Consent of Ernst &amp; Young LLP, Independent Auditors</FONT></TD>
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<TR BGCOLOR="#CCEEFF" VALIGN="TOP">
<TD WIDTH="9%" ALIGN="RIGHT"><FONT SIZE=2>23.2</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="89%"><FONT SIZE=2>Consent of WSGR (contained in Exhibit&nbsp;5.1)</FONT></TD>
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<TR BGCOLOR="White" VALIGN="TOP">
<TD WIDTH="9%" ALIGN="RIGHT"><FONT SIZE=2>24.1</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="89%"><FONT SIZE=2>Power of Attorney (see page&nbsp;4)</FONT></TD>
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<FONT SIZE=2><A HREF="#toc_ja1530_1">INFORMATION REQUIRED PURSUANT TO GENERAL INSTRUCTION E TO FORM S-8</A></FONT><BR>
<FONT SIZE=2><A HREF="#toc_ja1530_2">PART II INFORMATION REQUIRED IN THE REGISTRATION STATEMENT</A></FONT><BR>

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<FONT SIZE=2><A HREF="#toc_jc1530_1">SIGNATURES</A></FONT><BR>
<FONT SIZE=2><A HREF="#toc_jc1530_2">POWER OF ATTORNEY</A></FONT><BR>
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<FONT SIZE=2><A HREF="#toc_ka1530_1">INDEX TO EXHIBITS</A></FONT><BR>
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As filed with the Securities and Exchange Commission on June 20, 2001
Registration No. 333-
SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549
FORM S-8
REGISTRATION STATEMENT
UNDER
THE SECURITIES ACT OF 1933
NANOGEN, INC.
(Exact name of Registrant as specified in its charter)
Delaware
(State of incorporation)
10398 Pacific Center Court,
San Diego, CA 92121
33-0489621
(I.R.S. Employer Identification Number)
(Address,
including zip code, of Registrant's principal executive offices)
Nanogen,
Inc. 1997 Stock Incentive Plan, as amended
(Full
title of the plan)
Vera P. Pardee, Esq.
Vice President, General
Counsel and Secretary
10398 Pacific Center Court,
San Diego, CA 92121
(Name, address, including zip code, and telephone number, including area code, of agent for service)
Copy to:
John L. Donahue, Esq.
Wilson Sonsini Goodrich & Rosati
Professional Corporation
650 Page Mill Road
Palo Alto, CA 94304
(650) 493-9300
CALCULATION OF REGISTRATION FEE
Title of Securities to
be Registered
Amount
to be
Registered(1)
Proposed
Maximum
Offering Price Per
Share(2)
Proposed
Maximum
Aggregate
Offering Price
Amount of
Registration
Fee
Common Stock, par value $0.001, including related Series A Participating Preferred Stock Purchase Rights
1,500,000
$8.61
$12,915,000
$3,229
(1)
This
Registration Statement shall also cover any additional shares of Common Stock which become issuable by reason of any stock dividend, stock split, recapitalization or other
similar transaction effected without the receipt of consideration which results in an increase in the number of the outstanding shares of Common Stock.
(2)
Estimated
pursuant to Rule 457(h) under the Securities Act of 1933, as amended (the "Securities Act") solely for the purpose of calculating the registration fee.
INFORMATION REQUIRED PURSUANT TO GENERAL INSTRUCTION E TO FORM S-8
General Instruction E Information
This Registration Statement is being filed for the purpose of increasing the number of securities of the same class as other securities for which Registration
Statements of the Registrant on Form S-8 relating to the same employee benefit plan are effective. Registrant's Form S-8 Registration Statements filed with the Securities and Exchange
Commission on April 17, 1998 (No. 333-50381), July 29, 1999 (File No. 333-83993) and June 15, 2000 (File No. 333-39376) are hereby incorporated by reference.
PART II
INFORMATION REQUIRED IN THE REGISTRATION STATEMENT
Item 3.  Incorporation of Documents by Reference
There are hereby incorporated by reference into this Registration Statement and into the Prospectuses relating to this Registration Statement pursuant to
Rule 428 the following documents and information previously filed with the Securities and Exchange Commission:
1
The
Registrant's Annual Report on Form 10-K for the year ended December 31, 2000, filed pursuant to Section 13(a) of the Securities Exchange Act of 1934, as amended
('the Exchange Act') (File No. 0-23541);
2.
The
Registrant's Quarterly Report on Form 10-Q for the quarter ended March 31, 2001;
3.
The
description of Registrant's Common Stock contained in Registrant's Registration Statement on Form 8-A filed with the Commission on April 7, 1998; and
4.
The
description of the Preferred Stock Purchase Rights for Series A Participating Preferred Stock, par value $.001 per share of the Registrant contained in Registrant's
Registration Statement on Form 8-A filed November 24, 1998.
All
documents filed by the Registrant pursuant to Sections 13(a), 13(c), 14 and 15(d) of the Exchange Act after the date hereof, and prior to the filing of a post-effective amendment
which indicates that all securities offered have been sold or which deregisters all securities then remaining unsold, shall be deemed to be incorporated by reference herein and to be part hereof from
the date of filing of such documents.
Item 8.  Exhibits
Exhibit No.
Document
5.1
Opinion of Wilson Sonsini Goodrich & Rosati, Professional Corporation ('WSGR').
23.1
Consent of Ernst & Young LLP, Independent Auditors
23.2
Consent of WSGR (contained in Exhibit 5.1)
24.1
Power of Attorney (see page 4.)
Item 9.  Undertakings
(a) The
undersigned Registrant hereby undertakes:
(1) To
file, during any period in which offers or sales are being made, a post-effective amendment to this Registration Statement to include any material information
with respect to the plan of distribution not previously disclosed in the Registration Statement or any material change to such information in the Registration Statement.
1
(2) That, for the purpose of determining any liability under the Securities Act of 1933, as amended (the 'Securities Act'), each such post-effective amendment shall be
deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.
(3) To
remove from registration by means of a post-effective amendment any of the securities being registered which remain unsold at the termination of the offering.
(b) The
undersigned Registrant hereby undertakes that, for purposes of determining any liability under the Securities Act, each filing of the Registrant's annual report
pursuant to Section 13(a) or Section 15(d) of the Securities Exchange Act of 1934 that is incorporated by reference in the registration statement shall be deemed to be a new registration statement
relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.
(c) Insofar
as indemnification for liabilities arising under the Securities Act may be permitted to directors, officers and controlling persons of the Registrant
pursuant to the foregoing provisions, or otherwise, the Registrant has been advised that in the opinion of the Securities and Exchange Commission such indemnification is against public policy as
expressed in the Securities Act and is, therefore, unenforceable. In the event that a claim for indemnification against such liabilities (other than the payment by the Registrant of expenses incurred
or paid by a director, officer or controlling person of the Registrant in the successful defense of any action, suit or proceeding) is asserted by such director, officer or controlling person in
connection with the securities being registered, the Registrant will, unless in the opinion of its counsel the matter has been settled by controlling precedent, submit to a court of appropriate
jurisdiction the question whether such indemnification by it is against public policy as expressed in the Securities Act and will be governed by the final adjudication of such issue.
2
SIGNATURES
Pursuant to the requirements of the Securities Act of 1933, the Registrant, Nanogen, Inc., certifies that it has reasonable grounds to believe that it meets
all of the requirements for filing on Form S-8 and has duly caused this Registration Statement on Form S-8 to be signed on its behalf by the undersigned, thereunto duly authorized, in
the city of San Diego, State of California, on the 19th day of June, 2001.
NANOGEN, INC.
By:
/s/
VANCE RANDY WHITE
Vance Randy White
Chief Executive Officer
POWER OF ATTORNEY
KNOW ALL PERSONS BY THESE PRESENTS,
that each person whose signature appears below constitutes and appoints Kiernan T. Gallahue and
Vera P. Pardee and each of them, acting individually, as his attorney-in-fact, with full power of substitution, for him and in any and all capacities, to sign any and all amendments to this
Registration Statement on Form S-8 (including post-effective amendments) and to file the same, with all exhibits thereto and other documents in connection therewith, with the Securities and Exchange
Commission, hereby ratifying and confirming our signatures as they may be signed by our said attorney to any and all amendments to the Registration Statement on Form S-8.
Pursuant
to the requirements of the Securities Act of 1933, this Registration Statement on Form S-8 has been signed by the following persons in the capacities and on the dates
indicated.
Signature
Title
Date
/s/
VANCE RANDY WHITE
Vance Randy White
Chief Executive Officer and Director (Principal Executive Officer)
June 19, 2001
/s/
GERARD A. WILLS
Gerard A. Wills
Vice President, Chief Financial Officer and Treasurer (Principal Financial and Accounting Officer)
June 19, 2001
/s/
HOWARD C. BIRNDORF
Howard C. Birndorf
Chairman of the Board of Directors
June 19, 2001
/s/
VAL BUONAIUTO
Val Buonaiuto
Director
June 19, 2001
Cam L. Garner
Director
June  , 2001
Regina E. Herzlinger
Director
June  , 2001
/s/
DAVID G. LUDVIGSON
David G. Ludvigson
Director
June 19, 2001
Stelios B. Papadopoulos
Director
June  , 2001
3
INDEX TO EXHIBITS
Exhibit No.
Document
5.1
Opinion of Wilson Sonsini Goodrich & Rosati, Professional Corporation ('WSGR')
23.1
Consent of Ernst & Young LLP, Independent Auditors
23.2
Consent of WSGR (contained in Exhibit 5.1)
24.1
Power of Attorney (see page 4)
4
QuickLinks
INFORMATION REQUIRED PURSUANT TO GENERAL INSTRUCTION E TO FORM S-8
PART II INFORMATION REQUIRED IN THE REGISTRATION STATEMENT
SIGNATURES
POWER OF ATTORNEY
INDEX TO EXHIBITS