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

    <schemaVersion>X0202</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2007-06-28</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0000824068</issuerCik>
        <issuerName>ATS MEDICAL INC</issuerName>
        <issuerTradingSymbol>ATSI</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001399763</rptOwnerCik>
            <rptOwnerName>Alta Partners VIII, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3700</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001399894</rptOwnerCik>
            <rptOwnerName>Alta Partners Management VIII, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3700</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001198325</rptOwnerCik>
            <rptOwnerName>JANNEY DANIEL</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3700</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001198321</rptOwnerCik>
            <rptOwnerName>CHAMPSI FARAH</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3700</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>9800000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F1"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Warrant</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.65</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2008-06-28</value>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-06-28</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                    <footnoteId id="F3"/>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1960000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F1"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">These securities are held of record by Alta Partners VIII, L.P. (&quot;APVIII&quot;).  Alta Partners Management VIII, LLC (&quot;APMVIII&quot;) is the general partner of APVIII.  Guy Nohra, Daniel Janney and Farah Champsi are managing directors of APMVIII and exercise shared voting and investment power with respect to the shares owned by APVIII.  Each of the reporting persons disclaims beneficial ownership of such securities, except to the extent of his or its proportionate pecuniary interest therein.  Mr. Nohra, as a director of the Issuer, files Section 16 reports separately.</footnote>
        <footnote id="F2">The right represented by this warrant is exercisable, in whole or in part, at any time and from time to time from the earlier of (i) June 28, 2008, or (ii) the date on which the Issuer receives the requisite approval of its shareholders to issue shares of Common Stock upon exercise of this warrant (the &quot;Shareholder Approval&quot;), through June 28, 2014.</footnote>
        <footnote id="F3">If the Issuer has not received the Shareholder Approval, then ATVIII shall be entitled to receive, upon exercise of the warrant, in whole or in part, at any time and from time to time from June 28, 2008, cash from the Issuer in an amount equal to the difference between (A) the then-current fair market value of the Common Stock, and (B) the exercise price of the warrant, multiplied by the number of shares to which such exercise relates.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>By Alta Partners Management VIII, LLC, by /s/ Daniel Janney, managing director</signatureName>
        <signatureDate>2007-07-02</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Guy Nohra, Managing Director</signatureName>
        <signatureDate>2007-07-02</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Daniel Janney</signatureName>
        <signatureDate>2007-07-02</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Farah Champsi</signatureName>
        <signatureDate>2007-07-02</signatureDate>
    </ownerSignature>
</ownershipDocument>
