<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType><periodOfReport>2003-12-18</periodOfReport>
    <issuer>
        <issuerCik>0000716054</issuerCik>
        <issuerName>CYPRESS BIOSCIENCE INC</issuerName>
        <issuerTradingSymbol>cypb</issuerTradingSymbol></issuer><reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001205698</rptOwnerCik>
            <rptOwnerName>VAUGHN JACK H</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>1</isDirector><isOfficer>0</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther></reportingOwnerRelationship></reportingOwner><nonDerivativeTable><nonDerivativeTransaction><securityTitle><value>Common Stock</value></securityTitle><transactionDate><value>2003-12-18</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>7500</value></transactionShares><transactionPricePerShare><value>2.50</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>19625</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></nonDerivativeTransaction><nonDerivativeTransaction><securityTitle><value>Common Stock</value></securityTitle><transactionDate><value>2003-12-18</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>2500</value></transactionShares><transactionPricePerShare><value>2.51</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><postTransactionAmounts><sharesOwnedFollowingTransaction><value>22125</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></nonDerivativeTransaction></nonDerivativeTable><derivativeTable><derivativeTransaction><securityTitle><value>Stock Option (Right to Buy)</value></securityTitle><conversionOrExercisePrice><value>2.50</value></conversionOrExercisePrice><transactionDate><value>2003-12-18</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>1250</value></transactionShares><transactionPricePerShare><footnoteId id="F1"/></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>1995-06-26</value></exerciseDate><expirationDate><value>2005-06-26</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>1250</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></derivativeTransaction><derivativeTransaction><securityTitle><value>Stock Option (Right to Buy)</value></securityTitle><conversionOrExercisePrice><value>2.50</value></conversionOrExercisePrice><transactionDate><value>2003-12-18</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>1250</value></transactionShares><transactionPricePerShare><footnoteId id="F1"/></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>1998-06-30</value></exerciseDate><expirationDate><value>2006-06-27</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>1250</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></derivativeTransaction><derivativeTransaction><securityTitle><value>Stock Option (Right to Buy)</value></securityTitle><conversionOrExercisePrice><value>2.50</value></conversionOrExercisePrice><transactionDate><value>2003-12-18</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>1250</value></transactionShares><transactionPricePerShare><footnoteId id="F1"/></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>1997-10-15</value></exerciseDate><expirationDate><value>2006-06-27</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>1250</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></derivativeTransaction><derivativeTransaction><securityTitle><value>Stock Option (Right to Buy)</value></securityTitle><conversionOrExercisePrice><value>2.50</value></conversionOrExercisePrice><transactionDate><value>2003-12-18</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>1250</value></transactionShares><transactionPricePerShare><footnoteId id="F1"/></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>1996-04-15</value></exerciseDate><expirationDate><value>2006-04-15</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>1250</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></derivativeTransaction><derivativeTransaction><securityTitle><value>Stock Option (Right to Buy)</value></securityTitle><conversionOrExercisePrice><value>2.50</value></conversionOrExercisePrice><transactionDate><value>2003-12-18</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>1250</value></transactionShares><transactionPricePerShare><footnoteId id="F1"/></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>1999-09-14</value></exerciseDate><expirationDate><value>2006-06-27</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>1250</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></derivativeTransaction><derivativeTransaction><securityTitle><value>Stock Option (Right to Buy)</value></securityTitle><conversionOrExercisePrice><value>2.50</value></conversionOrExercisePrice><transactionDate><value>2003-12-18</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>1250</value></transactionShares><transactionPricePerShare><footnoteId id="F1"/></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2000-07-27</value></exerciseDate><expirationDate><value>2006-06-27</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>1250</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>0</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></derivativeTransaction><derivativeTransaction><securityTitle><value>Stock Option (Right to Buy)</value></securityTitle><conversionOrExercisePrice><value>2.51</value></conversionOrExercisePrice><transactionDate><value>2003-12-18</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>M</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>2500</value></transactionShares><transactionPricePerShare><footnoteId id="F1"/></transactionPricePerShare><transactionAcquiredDisposedCode><value>D</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2003-03-27</value><footnoteId id="F2"/></exerciseDate><expirationDate><value>2013-03-27</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>2500</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>61536</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></derivativeTransaction></derivativeTable><footnotes><footnote id="F1">Not Applicable</footnote><footnote id="F2">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><remarks/><ownerSignature><signatureName>Sabrina Martucci Johnson Attorney-in-Fact</signatureName><signatureDate>2003-12-18</signatureDate></ownerSignature></ownershipDocument>

