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<P ALIGN="CENTER"><FONT SIZE=2><B>As filed with the Securities and Exchange Commission on August&nbsp;16, 2002  </B></FONT></P>

<P ALIGN="RIGHT"><FONT SIZE=2><B> Registration No.&nbsp;333-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&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>  </B></FONT><FONT SIZE=2><B><I>Under<BR>
The Securities Act of 1933  </I></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="27%" ALIGN="CENTER"><FONT SIZE=2><B>Delaware<BR> </B></FONT><FONT SIZE=2>(State of incorporation)</FONT></TD>
<TD WIDTH="46%" ALIGN="CENTER"><FONT SIZE=2><B>10398 Pacific Center Court,<BR>
San Diego, CA 92121<BR> </B></FONT><FONT SIZE=2>(Address, including zip code, of Registrant's<BR>
principal executive offices)</FONT></TD>
<TD WIDTH="27%" ALIGN="CENTER"><FONT SIZE=2><B>33-0489621<BR> </B></FONT><FONT SIZE=2>(I.R.S. Employer<BR>
Identification Number)</FONT></TD>
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<P ALIGN="CENTER"><FONT SIZE=2><B>Nanogen, Inc. 2002 Stock Bonus Plan<BR>  </B></FONT><FONT SIZE=2>(Full title of the plan) </FONT></P>

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<P ALIGN="CENTER"><FONT SIZE=2><B>William Franzblau, Esq.<BR>
Vice President, Legal Affairs<BR>
10398 Pacific Center Court,<BR>
San Diego, CA 92121<BR>  </B></FONT><FONT SIZE=2>(Name, address, including zip code, and telephone number,<BR>
including area code, of agent for service) </FONT></P>

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<P ALIGN="CENTER"><FONT SIZE=2><I>Copy to:<BR>  </I></FONT><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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<TD COLSPAN=9 ALIGN="CENTER" VALIGN="BOTTOM"><FONT SIZE=2><B>CALCULATION OF REGISTRATION FEE</B></FONT></TD>
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<TD WIDTH="36%" ALIGN="CENTER" VALIGN="BOTTOM"><FONT SIZE=1><B>Title of Securities to 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 to be 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 Maximum Offering Price Per 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 Maximum Aggregate 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 Registration 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>250,000</FONT></TD>
<TD WIDTH="1%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="15%" ALIGN="CENTER"><FONT SIZE=2>$1.98</FONT></TD>
<TD WIDTH="1%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="15%" ALIGN="CENTER"><FONT SIZE=2>$495,000</FONT></TD>
<TD WIDTH="1%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD WIDTH="15%" ALIGN="CENTER"><FONT SIZE=2>$45.54</FONT></TD>
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<DL compact>
<DT style='margin-bottom:-11pt;'><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 style='margin-bottom:-11pt;'><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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<P ALIGN="CENTER"><FONT SIZE=2><A
NAME="de1701_information_required_pursuant___inf04911"> </A>
<A NAME="toc_de1701_1"> </A>
<BR></FONT><FONT SIZE=2><B>INFORMATION REQUIRED PURSUANT TO GENERAL INSTRUCTION E TO FORM S-8<BR>  <BR>    PART I<BR>  <BR>    INFORMATION REQUIRED IN THE SECTION 10(A) PROSPECTUS    <BR>  </B></FONT></P>

<P><FONT SIZE=2><A
NAME="de1701_item_1._plan_information."> </A>
<A NAME="toc_de1701_2"> </A></FONT> <FONT SIZE=2><B>Item 1. Plan Information.*    <BR>  </B></FONT></P>


<P><FONT SIZE=2><A
NAME="de1701_item_2._registrant_information__ite02342"> </A>
<A NAME="toc_de1701_3"> </A></FONT> <FONT SIZE=2><B>Item 2. Registrant Information and Employee Plan Information.*    <BR>  </B></FONT></P>

<DL compact>
<DT style='margin-bottom:-11pt;'><FONT SIZE=2>*</FONT></DT><DD><FONT SIZE=2>Information
required by Part&nbsp;I to be contained in the Section&nbsp;10(a) prospectus is omitted from this Registration Statement in accordance with Rule&nbsp;428 under the
Securities Act of 1933 and the Note to Part&nbsp;I of Form&nbsp;S-8. </FONT></DD></DL>
<P ALIGN="CENTER"><FONT SIZE=2><A
NAME="de1701_part_ii_information_req__de102465"> </A>
<A NAME="toc_de1701_4"> </A>
<BR></FONT><FONT SIZE=2><B>PART II<BR>  INFORMATION REQUIRED IN THE REGISTRATION STATEMENT    <BR>  </B></FONT></P>

<P><FONT SIZE=2><A
NAME="de1701_item_3._incorporation_of_documents_by_reference"> </A>
<A NAME="toc_de1701_5"> </A></FONT> <FONT SIZE=2><B>Item 3. Incorporation of Documents by Reference    <BR>  </B></FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;There are hereby incorporated by reference into this Registration Statement and into the Section&nbsp;10(a) Prospectus 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 style='margin-bottom:-11pt;'><FONT SIZE=2>1</FONT></DT><DD><FONT SIZE=2>The
Registrant's Annual Report on Form&nbsp;10-K for the year ended December&nbsp;31, 2001, 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 style='margin-bottom:-11pt;'><FONT SIZE=2>2.</FONT></DT><DD><FONT SIZE=2>The
Registrant's Quarterly Reports on Form&nbsp;10-Q for the quarter ended March&nbsp;31, 2002 and June&nbsp;30, 2002;
<BR><BR></FONT></DD><DT style='margin-bottom:-11pt;'><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 style='margin-bottom:-11pt;'><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;&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><A
NAME="de1701_item_4._description_of_securities"> </A>
<A NAME="toc_de1701_6"> </A>
<BR></FONT><FONT SIZE=2><B>Item 4. Description of Securities    <BR>  </B></FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not applicable. </FONT></P>

<P><FONT SIZE=2><A
NAME="de1701_item_5._interests_of_named_experts_and_counsel"> </A>
<A NAME="toc_de1701_7"> </A>
<BR></FONT><FONT SIZE=2><B>Item 5. Interests of Named Experts and Counsel    <BR>  </B></FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not applicable. </FONT></P>

<P><FONT SIZE=2><A
NAME="de1701_item_6._indemnification_of_directors_and_officers"> </A>
<A NAME="toc_de1701_8"> </A>
<BR></FONT><FONT SIZE=2><B>Item 6. Indemnification of Directors and Officers    <BR>  </B></FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Section&nbsp;145 of the Delaware General Corporation Law provides for the indemnification of officers, directors, and other corporate agents in terms
sufficiently broad to indemnify such persons under certain circumstances for liabilities (including reimbursement for expenses incurred) arising under the Securities Act of 1933, as amended (the
"Act"). Article&nbsp;XI of the Registrant's Restated Certificate of Incorporation (Exhibit&nbsp;3.(i)(1) to the Registrant's Form&nbsp;10-K for the year ended December&nbsp;31,
1998) </FONT></P>

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

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<P><FONT SIZE=2>
and Article&nbsp;VI of the Registrant's Bylaws (Exhibit&nbsp;3.(ii)1 to the Registrant's Form&nbsp;10-Q for the quarter ended September&nbsp;30, 2001) provide for indemnification
of the Registrant's directors, officers, employees and other agents to the extent and under the circumstances permitted by the Delaware General Corporation Law. The Registrant has also entered into
agreements with its directors and officers that will require the Registrant, among other things, to indemnify them against certain liabilities that may arise by reason of their status or service as
directors or officers to the fullest extent not prohibited by law (Exhibit&nbsp;10.7 to the Registrant's on Form&nbsp;S-1 (File No.&nbsp;333-42791)). </FONT></P>


<P><FONT SIZE=2><A
NAME="de1701_item_7._exemption_from_registration_claimed"> </A>
<A NAME="toc_de1701_9"> </A>
<BR></FONT><FONT SIZE=2><B>Item 7. Exemption from Registration Claimed    <BR>  </B></FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not applicable. </FONT></P>

<P><FONT SIZE=2><A
NAME="de1701_item_8._exhibits"> </A>
<A NAME="toc_de1701_10"> </A>
<BR></FONT><FONT SIZE=2><B>Item 8. Exhibits    <BR>  </B></FONT></P>

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<TH WIDTH="10%" ALIGN="CENTER"><FONT SIZE=1><B>Exhibit<BR>
Number</B></FONT><HR NOSHADE></TH>
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<TH WIDTH="88%" ALIGN="CENTER"><FONT SIZE=1><B>Document</B></FONT><HR NOSHADE></TH>
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<TD WIDTH="10%" ALIGN="RIGHT"><FONT SIZE=2><BR>
5.1</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="88%"><FONT SIZE=2><BR>
Opinion of Wilson Sonsini Goodrich &amp; Rosati, Professional Corporation ("WSGR").</FONT></TD>
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<TD WIDTH="10%" ALIGN="RIGHT"><FONT SIZE=2><BR>
10.1</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="88%"><FONT SIZE=2><BR>
2002 Stock Bonus Plan(1)</FONT></TD>
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<TD WIDTH="10%" ALIGN="RIGHT"><FONT SIZE=2><BR>
23.1</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="88%"><FONT SIZE=2><BR>
Consent of Ernst &amp; Young LLP, Independent Auditors</FONT></TD>
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<TD WIDTH="10%" ALIGN="RIGHT"><FONT SIZE=2><BR>
23.2</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="88%"><FONT SIZE=2><BR>
Consent of WSGR (contained in Exhibit 5.1)</FONT></TD>
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<TD WIDTH="10%" ALIGN="RIGHT"><FONT SIZE=2><BR>
24.1</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="88%"><FONT SIZE=2><BR>
Power of Attorney (see page 4.)</FONT></TD>
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<DL compact>
<DT style='margin-bottom:-11pt;'><FONT SIZE=2>(1)</FONT></DT><DD><FONT SIZE=2>Incorporated
by reference to Exhibit&nbsp;10.10 to the Registrant's Quarterly Report on Form&nbsp;10-Q for the quarter ended June&nbsp;30, 2002. </FONT></DD></DL>

<P><FONT SIZE=2><A
NAME="de1701_item_9._undertakings"> </A>
<A NAME="toc_de1701_11"> </A>
<BR></FONT><FONT SIZE=2><B>Item 9. Undertakings    <BR>  </B></FONT></P>

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

<UL>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(1)&nbsp;&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>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(2)&nbsp;&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;&nbsp;&nbsp;&nbsp;&nbsp;(3)&nbsp;&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;&nbsp;&nbsp;&nbsp;&nbsp;(b)&nbsp;&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&nbsp;13(a) or Section&nbsp;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;&nbsp;&nbsp;&nbsp;&nbsp;(c)&nbsp;&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 </FONT></P>

<P ALIGN="CENTER"><FONT SIZE=2>3</FONT></P>

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<P><FONT SIZE=2>
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>4</FONT></P>

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<P ALIGN="CENTER"><FONT SIZE=2><A
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<A NAME="toc_dg1701_1"> </A>
<BR></FONT><FONT SIZE=2><B>SIGNATURES    <BR>  </B></FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Act of 1933, the Registrant, Nanogen,&nbsp;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 15th day of August, 2002. </FONT></P>

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<TD WIDTH="3%"><FONT SIZE=2>&nbsp;</FONT></TD>
<TD COLSPAN=3><FONT SIZE=2>NANOGEN, INC.</FONT></TD>
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<TD WIDTH="45%"><FONT SIZE=2><BR>
&nbsp;</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="5%"><FONT SIZE=2><BR>
By:</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="45%"><FONT SIZE=2><BR>
/s/ HOWARD C. BIRNDORF</FONT><HR NOSHADE><FONT SIZE=2> Howard C. Birndorf<BR>
Executive Chairman</FONT></TD>
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<P ALIGN="CENTER"><FONT SIZE=2><A
NAME="dg1701_power_of_attorney"> </A>
<A NAME="toc_dg1701_2"> </A>
<BR></FONT><FONT SIZE=2><B>POWER OF ATTORNEY    <BR>  </B></FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&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 Gerard
A. Wills and William Franzblau 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&nbsp;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 said attorney to any and all amendments to the
Registration Statement on Form&nbsp;S-8. </FONT></P>

<P><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant
to the requirements of the Securities Act of 1933, this Registration Statement on Form&nbsp;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="37%" ALIGN="CENTER"><FONT SIZE=1><B>Signature</B></FONT><HR NOSHADE></TH>
<TH WIDTH="2%"><FONT SIZE=1>&nbsp;</FONT></TH>
<TH WIDTH="37%" ALIGN="CENTER"><FONT SIZE=1><B>Title</B></FONT><HR NOSHADE></TH>
<TH WIDTH="2%"><FONT SIZE=1>&nbsp;</FONT></TH>
<TH WIDTH="21%" ALIGN="CENTER"><FONT SIZE=1><B>Date</B></FONT><HR NOSHADE></TH>
</TR>
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<TD WIDTH="37%"><FONT SIZE=2><BR>
/s/&nbsp;&nbsp;</FONT><FONT SIZE=2>HOWARD C. BIRNDORF</FONT><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT><HR NOSHADE><FONT SIZE=2> Howard C. Birndorf</FONT></TD>
<TD WIDTH="2%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="37%"><FONT SIZE=2><BR>
Executive Chairman and Chairman of the Board of Directors (Principal Executive Officer)</FONT></TD>
<TD WIDTH="2%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="21%"><FONT SIZE=2><BR>
August 15, 2002</FONT></TD>
</TR>
<TR VALIGN="TOP">
<TD WIDTH="37%"><FONT SIZE=2><BR>
/s/&nbsp;&nbsp;</FONT><FONT SIZE=2>GERARD A. WILLS</FONT><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT><HR NOSHADE><FONT SIZE=2> Gerard A. Wills</FONT></TD>
<TD WIDTH="2%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="37%"><FONT SIZE=2><BR>
Vice President, Chief Financial Officer and Treasurer (Principal Financial and Accounting Officer)</FONT></TD>
<TD WIDTH="2%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="21%"><FONT SIZE=2><BR>
August 15, 2002</FONT></TD>
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<TD WIDTH="37%"><FONT SIZE=2><BR>
&nbsp;&nbsp;&nbsp;&nbsp;</FONT><HR NOSHADE><FONT SIZE=2> Val Buonaiuto</FONT></TD>
<TD WIDTH="2%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="37%"><FONT SIZE=2><BR>
Director</FONT></TD>
<TD WIDTH="2%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="21%"><FONT SIZE=2><BR>
August&nbsp;&nbsp;&nbsp;&nbsp;, 2002</FONT></TD>
</TR>
<TR VALIGN="BOTTOM">
<TD WIDTH="37%" VALIGN="TOP"><FONT SIZE=2><BR>
/s/&nbsp;&nbsp;</FONT><FONT SIZE=2>DAVID G. LUDVIGSON</FONT><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT><HR NOSHADE><FONT SIZE=2> David G. Ludvigson</FONT></TD>
<TD WIDTH="2%" VALIGN="TOP"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="37%" VALIGN="TOP"><FONT SIZE=2><BR>
Director</FONT></TD>
<TD WIDTH="2%" VALIGN="TOP"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="21%" VALIGN="TOP"><FONT SIZE=2><BR>
August 15, 2002</FONT></TD>
</TR>
<TR VALIGN="BOTTOM">
<TD WIDTH="37%" VALIGN="TOP"><FONT SIZE=2><BR>
/s/&nbsp;&nbsp;</FONT><FONT SIZE=2>STELIOS B. PAPADOPOULOS</FONT><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT><HR NOSHADE><FONT SIZE=2> Stelios B. Papadopoulos</FONT></TD>
<TD WIDTH="2%" VALIGN="TOP"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="37%" VALIGN="TOP"><FONT SIZE=2><BR>
Director</FONT></TD>
<TD WIDTH="2%" VALIGN="TOP"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="21%" VALIGN="TOP"><FONT SIZE=2><BR>
August 15, 2002</FONT></TD>
</TR>
<TR VALIGN="BOTTOM">
<TD WIDTH="37%" VALIGN="TOP"><FONT SIZE=2><BR>
/s/&nbsp;&nbsp;</FONT><FONT SIZE=2>ROBERT E. WHALEN</FONT><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT><HR NOSHADE><FONT SIZE=2> Robert E. Whalen</FONT></TD>
<TD WIDTH="2%" VALIGN="TOP"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="37%" VALIGN="TOP"><FONT SIZE=2><BR>
Director</FONT></TD>
<TD WIDTH="2%" VALIGN="TOP"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="21%" VALIGN="TOP"><FONT SIZE=2><BR>
August 15, 2002</FONT></TD>
</TR>
<TR VALIGN="BOTTOM">
<TD WIDTH="37%" VALIGN="TOP"><FONT SIZE=2><BR>
/s/&nbsp;&nbsp;</FONT><FONT SIZE=2>DR. VANCE R. WHITE</FONT><FONT SIZE=2>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</FONT><HR NOSHADE><FONT SIZE=2> Dr. Vance R. White</FONT></TD>
<TD WIDTH="2%" VALIGN="TOP"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="37%" VALIGN="TOP"><FONT SIZE=2><BR>
Director</FONT></TD>
<TD WIDTH="2%" VALIGN="TOP"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="21%" VALIGN="TOP"><FONT SIZE=2><BR>
August 15, 2002</FONT></TD>
</TR>
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<P ALIGN="CENTER"><FONT SIZE=2>5</FONT></P>

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<TH WIDTH="10%" ALIGN="CENTER"><FONT SIZE=1><B>Exhibit<BR>
Number</B></FONT><HR NOSHADE></TH>
<TH WIDTH="3%"><FONT SIZE=1>&nbsp;</FONT></TH>
<TH WIDTH="88%" ALIGN="CENTER"><FONT SIZE=1><B>Document</B></FONT><HR NOSHADE></TH>
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5.1</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="88%"><FONT SIZE=2><BR>
Opinion of Wilson Sonsini Goodrich &amp; Rosati, Professional Corporation ("WSGR")</FONT></TD>
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<TD WIDTH="10%" ALIGN="RIGHT"><FONT SIZE=2><BR>
23.1</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="88%"><FONT SIZE=2><BR>
Consent of Ernst &amp; Young LLP, Independent Auditors</FONT></TD>
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23.2</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="88%"><FONT SIZE=2><BR>
Consent of WSGR (contained in Exhibit 5.1)</FONT></TD>
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<TD WIDTH="10%" ALIGN="RIGHT"><FONT SIZE=2><BR>
24.1</FONT></TD>
<TD WIDTH="3%"><FONT SIZE=2><BR>&nbsp;</FONT></TD>
<TD WIDTH="88%"><FONT SIZE=2><BR>
Power of Attorney (see page 4)</FONT></TD>
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<P><br><A NAME="02SAN1701_1">QuickLinks</A><br></P><!-- TOC_BEGIN -->
<FONT SIZE=2><A HREF="#toc_de1701_1">INFORMATION REQUIRED PURSUANT TO GENERAL INSTRUCTION E TO FORM S-8 PART I INFORMATION REQUIRED IN THE SECTION 10(A) PROSPECTUS</A></FONT><BR>
<UL>
<FONT SIZE=2><A HREF="#toc_de1701_2">Item 1. Plan Information.</A></FONT><BR>
<FONT SIZE=2><A HREF="#toc_de1701_3">Item 2. Registrant Information and Employee Plan Information.</A></FONT><BR>
</UL>
<FONT SIZE=2><A HREF="#toc_de1701_4">PART II INFORMATION REQUIRED IN THE REGISTRATION STATEMENT</A></FONT><BR>
<UL>
<FONT SIZE=2><A HREF="#toc_de1701_5">Item 3. Incorporation of Documents by Reference</A></FONT><BR>
<FONT SIZE=2><A HREF="#toc_de1701_6">Item 4. Description of Securities</A></FONT><BR>
<FONT SIZE=2><A HREF="#toc_de1701_7">Item 5. Interests of Named Experts and Counsel</A></FONT><BR>
<FONT SIZE=2><A HREF="#toc_de1701_8">Item 6. Indemnification of Directors and Officers</A></FONT><BR>
<FONT SIZE=2><A HREF="#toc_de1701_9">Item 7. Exemption from Registration Claimed</A></FONT><BR>
<FONT SIZE=2><A HREF="#toc_de1701_10">Item 8. Exhibits</A></FONT><BR>
<FONT SIZE=2><A HREF="#toc_de1701_11">Item 9. Undertakings</A></FONT><BR>
</UL>

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<FONT SIZE=2><A HREF="#toc_dg1701_1">SIGNATURES</A></FONT><BR>
<FONT SIZE=2><A HREF="#toc_dg1701_2">POWER OF ATTORNEY</A></FONT><BR>
<FONT SIZE=2><A HREF="#toc_dg1701_3">INDEX TO EXHIBITS</A></FONT><BR>
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As filed with the Securities and Exchange Commission on August 16, 2002
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
(Address, including zip code, of Registrant's
principal executive offices)
33-0489621
(I.R.S. Employer
Identification Number)
Nanogen, Inc. 2002 Stock Bonus Plan
(Full title of the plan)
William Franzblau, Esq.
Vice President, Legal Affairs
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
250,000
$1.98
$495,000
$45.54
(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
PART I
INFORMATION REQUIRED IN THE SECTION 10(A) PROSPECTUS
Item 1. Plan Information.*
Item 2. Registrant Information and Employee Plan Information.*
*
Information
required by Part I to be contained in the Section 10(a) prospectus is omitted from this Registration Statement in accordance with Rule 428 under the
Securities Act of 1933 and the Note to Part I of Form S-8.
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 Section 10(a) Prospectus 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, 2001, 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 Reports on Form 10-Q for the quarter ended March 31, 2002 and June 30, 2002;
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 4. Description of Securities
Not applicable.
Item 5. Interests of Named Experts and Counsel
Not applicable.
Item 6. Indemnification of Directors and Officers
Section 145 of the Delaware General Corporation Law provides for the indemnification of officers, directors, and other corporate agents in terms
sufficiently broad to indemnify such persons under certain circumstances for liabilities (including reimbursement for expenses incurred) arising under the Securities Act of 1933, as amended (the
"Act"). Article XI of the Registrant's Restated Certificate of Incorporation (Exhibit 3.(i)(1) to the Registrant's Form 10-K for the year ended December 31,
1998)
2
and Article VI of the Registrant's Bylaws (Exhibit 3.(ii)1 to the Registrant's Form 10-Q for the quarter ended September 30, 2001) provide for indemnification
of the Registrant's directors, officers, employees and other agents to the extent and under the circumstances permitted by the Delaware General Corporation Law. The Registrant has also entered into
agreements with its directors and officers that will require the Registrant, among other things, to indemnify them against certain liabilities that may arise by reason of their status or service as
directors or officers to the fullest extent not prohibited by law (Exhibit 10.7 to the Registrant's on Form S-1 (File No. 333-42791)).
Item 7. Exemption from Registration Claimed
Not applicable.
Item 8. Exhibits
Exhibit
Number
Document
5.1
Opinion of Wilson Sonsini Goodrich & Rosati, Professional Corporation ("WSGR").
10.1
2002 Stock Bonus Plan(1)
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.)
(1)
Incorporated
by reference to Exhibit 10.10 to the Registrant's Quarterly Report on Form 10-Q for the quarter ended June 30, 2002.
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.
(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
3
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.
4
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 15th day of August, 2002.
NANOGEN, INC.
By:
/s/ HOWARD C. BIRNDORF
Howard C. Birndorf
Executive Chairman
POWER OF ATTORNEY
KNOW ALL PERSONS BY THESE PRESENTS
, that each person whose signature appears below constitutes and appoints Gerard
A. Wills and William Franzblau 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 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/
HOWARD C. BIRNDORF
Howard C. Birndorf
Executive Chairman and Chairman of the Board of Directors (Principal Executive Officer)
August 15, 2002
/s/
GERARD A. WILLS
Gerard A. Wills
Vice President, Chief Financial Officer and Treasurer (Principal Financial and Accounting Officer)
August 15, 2002
Val Buonaiuto
Director
August    , 2002
/s/
DAVID G. LUDVIGSON
David G. Ludvigson
Director
August 15, 2002
/s/
STELIOS B. PAPADOPOULOS
Stelios B. Papadopoulos
Director
August 15, 2002
/s/
ROBERT E. WHALEN
Robert E. Whalen
Director
August 15, 2002
/s/
DR. VANCE R. WHITE
Dr. Vance R. White
Director
August 15, 2002
5
INDEX TO EXHIBITS
Exhibit
Number
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)
QuickLinks
INFORMATION REQUIRED PURSUANT TO GENERAL INSTRUCTION E TO FORM S-8 PART I INFORMATION REQUIRED IN THE SECTION 10(A) PROSPECTUS
Item 1. Plan Information.
Item 2. Registrant Information and Employee Plan Information.
PART II INFORMATION REQUIRED IN THE REGISTRATION STATEMENT
Item 3. Incorporation of Documents by Reference
Item 4. Description of Securities
Item 5. Interests of Named Experts and Counsel
Item 6. Indemnification of Directors and Officers
Item 7. Exemption from Registration Claimed
Item 8. Exhibits
Item 9. Undertakings
SIGNATURES
POWER OF ATTORNEY
INDEX TO EXHIBITS