-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
Originator-Key-Asymmetric:
 MFgwCgYEVQgBAQICAf8DSgAwRwJAW2sNKK9AVtBzYZmr6aGjlWyK3XmZv3dTINen
 TWSM7vrzLADbmYQaionwg5sDW3P6oaM5D3tdezXMm7z1T+B+twIDAQAB
MIC-Info: RSA-MD5,RSA,
 KAs1xGRLd5GZTsvODoiWIfEbFa08t9IvmC/kn6l/urJ5JQzcxyJKCI1aILamtrzp
 j2Xjfyg5J5O7r62GBueoHQ==

<SEC-DOCUMENT>0001181431-08-026379.txt : 20080423
<SEC-HEADER>0001181431-08-026379.hdr.sgml : 20080423
<ACCEPTANCE-DATETIME>20080423203951
ACCESSION NUMBER:		0001181431-08-026379
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20080402
FILED AS OF DATE:		20080423
DATE AS OF CHANGE:		20080423

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			BIRNDORF HOWARD C
		CENTRAL INDEX KEY:			0001078432

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-23541
		FILM NUMBER:		08772861

	BUSINESS ADDRESS:	
		BUSINESS PHONE:		6195467700

	MAIL ADDRESS:	
		STREET 1:		C/O NANOGEN INC
		STREET 2:		10398 PACIFIC CENTER COURT
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			NANOGEN INC
		CENTRAL INDEX KEY:			0001030339
		STANDARD INDUSTRIAL CLASSIFICATION:	LABORATORY ANALYTICAL INSTRUMENTS [3826]
		IRS NUMBER:				330489621
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		10398 PACIFIC CENTER COURT
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121
		BUSINESS PHONE:		858 410 4600

	MAIL ADDRESS:	
		STREET 1:		10398 PACIFIC CENTER COURT
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>rrd203633.xml
<DESCRIPTION>04-02-08 PERFORMANCE OPTIONS
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2008-04-02</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001030339</issuerCik>
        <issuerName>NANOGEN INC</issuerName>
        <issuerTradingSymbol>NGEN</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001078432</rptOwnerCik>
            <rptOwnerName>BIRNDORF HOWARD C</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>10398 PACIFIC CENTER CT.</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92121</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Executive Chairman and CEO</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Performance Stock Option</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>.4158</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2008-04-02</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>547500</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2018-01-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>547500</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>547500</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">These performance-based options were approved by the board of directors of Issuer on January 1, 2008 (&quot;Grant Date&quot;), subject to shareholder approval of amendment of the stock option plan (the &quot;Amended Plan&quot;) under which such options were granted.  The option shares are awarded upon achievement of certain goals under the Issuer's bonus plan for the prior fiscal year at above-target levels.  The options vested over a 4-year period, with 25% of options shares to vest upon completion of one year of service following the Grant Date, and the remaining option shares vest monthly over a 36-month period measured from the first anniversary of the Grant Date.  The Issuer's shareholders approved the Amended Plan on April 2, 2008.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/S/ Howard Birndorf</signatureName>
        <signatureDate>2008-04-23</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
-----END PRIVACY-ENHANCED MESSAGE-----