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

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2010-11-18</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001421419</issuerCik>
        <issuerName>AGA Medical Holdings, Inc.</issuerName>
        <issuerTradingSymbol>AGAM</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001324863</rptOwnerCik>
            <rptOwnerName>Thompson Tommy G</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1333 NEW HAMPSHIRE AVENUE NW</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 430</rptOwnerStreet2>
            <rptOwnerCity>WASHINGTON</rptOwnerCity>
            <rptOwnerState>DC</rptOwnerState>
            <rptOwnerZipCode>20036</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>2010-11-18</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>U</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>1000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>20.80</value>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By spouse</value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>2006 Equity Incentive Plan options (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>7.15</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2010-11-18</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>413320</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>13.65</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2015-07-28</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>413320</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>2008 Equity Incentive Plan options (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>14.93</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2010-11-18</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>7692</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>5.87</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2017-01-04</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>7692</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">Disposition of 1,000 shares of common stock in exchange for per share consideration of $20.80 in an exchange offer by St. Jude Medical, Inc. (&quot;St. Jude Medical&quot;) pursuant to the terms of the Agreement and Plan of Merger and Reorganization (the &quot;Merger Agreement&quot;), dated October 15, 2010, among AGA Medical Holdings, Inc. (&quot;AGA&quot;), St. Jude Medical and Asteroid Subsidiary Corporation.  Pursuant to the terms of the Merger Agreement and the exchange offer, AGA stockholders could elect to receive the following consideration for each share of AGA common stock tendered in the exchange offer: (i) $20.80 in cash, without interest (&quot;Cash Consideration&quot;); or (ii) stock consideration of 0.540 shares of St. Jude Medical common stock (the &quot;Stock Consideration&quot;). AGA stockholders could elect to receive Cash Consideration for some shares and Stock Consideration for others, subject to possible proration. St. Jude Medical expects to announce the final proration calculations no later 11/23/10.</footnote>
        <footnote id="F2">This option was canceled pursuant to the terms of the Merger Agreement in exchange for a cash payment representing the difference between the per share exercise price of the option and the cash merger consideration of $20.80 per share, multiplied by the number of shares of AGA common stock underlying the option.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Brigid A. Makes as attorney-in-fact for Tommy G. Thompson pursuant to Power of Attorney previously filed.</signatureName>
        <signatureDate>2010-11-18</signatureDate>
    </ownerSignature>
</ownershipDocument>
