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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
 T6owYhKUiy/zDSgmtApbIQLwZ9lDJV/NRKIJ9lxxpsy1sfzUqc45g/BRQiwOPAGJ
 +UDkrBwoxWVBZtIivtAUew==

<SEC-DOCUMENT>0000716054-06-000012.txt : 20060104
<SEC-HEADER>0000716054-06-000012.hdr.sgml : 20060104
<ACCEPTANCE-DATETIME>20060104150134
ACCESSION NUMBER:		0000716054-06-000012
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20060102
FILED AS OF DATE:		20060104
DATE AS OF CHANGE:		20060104

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			WOOLARD DENISE
		CENTRAL INDEX KEY:			0001279110

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-12943
		FILM NUMBER:		06506841

	MAIL ADDRESS:	
		STREET 1:		4350 EXECUTIVE DR
		STREET 2:		STE 325
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			CYPRESS BIOSCIENCE INC
		CENTRAL INDEX KEY:			0000716054
		STANDARD INDUSTRIAL CLASSIFICATION:	BIOLOGICAL PRODUCTS (NO DIAGNOSTIC SUBSTANCES) [2836]
		IRS NUMBER:				222389839
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		4350 EXECUTIVE DRIVE,SUITE 325
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121
		BUSINESS PHONE:		8584522323

	MAIL ADDRESS:	
		STREET 1:		4350 EXECUTIVE DRIVE,SUITE 325
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	IMRE CORP
		DATE OF NAME CHANGE:	19920703
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2006-01-02</periodOfReport>

    <issuer>
        <issuerCik>0000716054</issuerCik>
        <issuerName>CYPRESS BIOSCIENCE INC</issuerName>
        <issuerTradingSymbol>CYPB</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001279110</rptOwnerCik>
            <rptOwnerName>WOOLARD DENISE</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>4350 EXECUTIVE DRIVE SUITE 325</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92121</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>VP, Legal &amp; Business Affairs</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>5.78</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2006-01-02</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>30000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2016-01-02</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>30000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>30000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">50% of the shares subject to the option shall vest daily and ratably during 2006, and the remaining 50% shall vest daily and ratably over the next three years, such that the option shall be fully vested on January 2, 2010.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Sabrina Martucci Johnson Attorney-in-Fact</signatureName>
        <signatureDate>2006-01-04</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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