<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2004-12-10</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001067588</issuerCik>
        <issuerName>ACLARA BIOSCIENCES INC</issuerName>
        <issuerTradingSymbol>ACLA</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001226863</rptOwnerCik>
            <rptOwnerName>KLOPACK THOMAS G</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1288 PEAR AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>MOUNTAIN VIEW</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94043</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Executive Officer</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2004-12-10</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>15000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>NSO Stock Option</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>2.02</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2004-12-10</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>507738</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>2.02</value>
                    <footnoteId id="F3"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2004-03-20</value>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2013-03-20</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>common stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>507738</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Incentive Stock Option</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>2.02</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2004-12-10</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>192262</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>2.02</value>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2004-03-20</value>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2013-03-20</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>common stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>192262</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Incentive Stock Option</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.20</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2004-12-10</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>8841</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>3.20</value>
                    <footnoteId id="F4"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2005-02-06</value>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-02-06</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>common stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>8841</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>NSO Stock Option</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.20</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2004-12-10</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>116159</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>3.20</value>
                    <footnoteId id="F5"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2005-02-06</value>
                <footnoteId id="F5"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-02-06</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>common stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>116159</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Disposed of pursuant to merger agreement between Aclara Biosciences, Inc., and Virologic, Inc., in exchange for 25,500 shares of Virologic, Inc. Common Stock.</footnote>
        <footnote id="F2">This option, which provided for monthly vesting after one year cliff beginning 3/20/2003, was assumed by Virologic, Inc., in the merger and replaced with an option to purchase 326,845 shares of Virologic common stock for $1.19.</footnote>
        <footnote id="F3">This option, which provided for monthly vesting after one year cliff beginning 3/20/2003, was assumed by Virologic, Inc., in the merger and replaced with an option to purchase 863,154 shares of Virologic common stock for $1.19.</footnote>
        <footnote id="F4">This option, which provided for monthly vesting after one year cliff beginning 2/6/2004, was assumed by Virologic, Inc., in the merger and replaced with an option to purchase 15,029 shares of Virologic common stock for $1.88.</footnote>
        <footnote id="F5">This option, which provided for monthly vesting after one year cliff beginning 2/6/2004, was assumed by Virologic, Inc., in the merger and replaced with an option to purchase 197,470 shares of Virologic common stock for $1.88.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Dian Georgia, attorney-in-fact</signatureName>
        <signatureDate>2004-12-10</signatureDate>
    </ownerSignature>
</ownershipDocument>

