<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0101</schemaVersion>

    <documentType>4</documentType><periodOfReport>2003-07-22</periodOfReport>
    <issuer>
        <issuerCik>0000716054</issuerCik>
        <issuerName>CYPRESS BIOSCIENCE INC</issuerName>
        <issuerTradingSymbol>cypb</issuerTradingSymbol></issuer><reportingOwner><reportingOwnerId>
            <rptOwnerCik>0001205698</rptOwnerCik>
            <rptOwnerName>VAUGHN JACK A</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>  </rptOwnerStreet1>
            <rptOwnerStreet2>  </rptOwnerStreet2>
            <rptOwnerCity>  </rptOwnerCity>
            <rptOwnerState>  </rptOwnerState>
            <rptOwnerZipCode>  </rptOwnerZipCode>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>1</isDirector><isOfficer>0</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther></reportingOwnerRelationship></reportingOwner><nonDerivativeSecurity><securityTitle><value>Common Stock</value></securityTitle><transactionDate><value>2003-07-22</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>10000</value></transactionShares><transactionValue><value>2.51</value></transactionValue><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>14780</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></nonDerivativeSecurity><derivativeSecurity><securityTitle><value>Stock Option (Right to Buy)</value></securityTitle><conversionOrExercisePrice><value>2.51</value></conversionOrExercisePrice><transactionDate><value>2003-07-22</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>10000</value></transactionShares><transactionValue><value>0</value></transactionValue><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2003-03-27</value><footnoteId id="F1"/></exerciseDate><expirationDate><value>2013-03-27</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>10000</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>64036</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></derivativeSecurity><footnotes><footnote id="F1">Twenty-five thousand (25,000) of the shares subject to the option vested on March 27, 2003 with the remainder vesting thereafter on a daily basis over four years, such that all shares subject to the option will be fully vested and exercisable as of March 27, 2007.</footnote></footnotes><ownerSignature><signatureName>Sabrina Martucci Johnson  Attorney-in-Fact</signatureName><signatureDate>2003-07-23</signatureDate></ownerSignature></ownershipDocument>

