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

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2010-10-27</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001338042</issuerCik>
        <issuerName>Aegerion Pharmaceuticals, Inc.</issuerName>
        <issuerTradingSymbol>AEGR</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001257444</rptOwnerCik>
            <rptOwnerName>ALTA BIOPHARMA PARTNERS III LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SUITE 3700</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>0001280234</rptOwnerCik>
            <rptOwnerName>ALTA BIOPHARMA MANAGEMENT III LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SUITE 3700</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>0001280265</rptOwnerCik>
            <rptOwnerName>ALTA BIOPHARMA PARTNERS III GMBH &amp; CO BETEILIGUNGS KG</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SUITE 3700</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>0001280238</rptOwnerCik>
            <rptOwnerName>ALTA EMBARCADERO BIOPHARMA PARTNERS III LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SUITE 3700</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>0001198323</rptOwnerCik>
            <rptOwnerName>DELEAGE JEAN</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>94132</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001198332</rptOwnerCik>
            <rptOwnerName>PENHOET EDWARD</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>0001211840</rptOwnerCik>
            <rptOwnerName>HURWITZ EDWARD</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER, SUITE 3700</rptOwnerStreet1>
            <rptOwnerStreet2></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>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2010-10-27</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>C</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
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                </transactionShares>
                <transactionPricePerShare>
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                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
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                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
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                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
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                    <footnoteId id="F3"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
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            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
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            </transactionCoding>
            <transactionTimeliness>
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            </transactionTimeliness>
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                </transactionShares>
                <transactionPricePerShare>
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                <transactionAcquiredDisposedCode>
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                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1465881</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
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        <nonDerivativeTransaction>
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            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
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            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
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                </sharesOwnedFollowingTransaction>
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        <nonDerivativeTransaction>
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            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
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                </sharesOwnedFollowingTransaction>
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        </nonDerivativeTransaction>
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            </transactionDate>
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        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Upon the closing of the Issuer's initial public offering on October 27, 2010, each share of Series A Convertible Preferred Stock (the &quot;Series A Shares&quot;), plus accrued dividends, automatically converted into shares of common stock of the Issuer in accordance with the terms of the Issuer's Third Amended and Restated Certificate of Incorporation. Each Series A Share converted into 0.38701117412 shares of common stock.</footnote>
        <footnote id="F2">Alta BioPharma Management III, LLC (&quot;ABMIII&quot;) is the general partner of ABPIII and the managing limited partner of Alta BioPharma Partners III GmbH &amp; Co. Beteiligungs KG (&quot;ABPIIIKG&quot;).  Jean Deleage, Farah Champsi, Edward Penhoet and Edward Hurwitz are the directors of ABMIII and managers of Alta Embarcadero BioPharma Partners III, LLC (&quot;AEBPIII&quot;).  Alison Kiley, a director of the Issuer, is a member of ABMIII and may be deemed to share investment power over the securities of the Issuer held by ABPIII, ABPIIIKG and AEBPIII with the directors of ABMIII and managers of AEBPIII.  Each of Dr. Deleage, Ms. Champsi, Dr. Penhoet and Mr. Hurwitz disclaim beneficial ownership of such securities except to the extent of his or her pecuniary interest therein.</footnote>
        <footnote id="F3">These securities are owned directly by ABPIII.</footnote>
        <footnote id="F4">Upon the closing of the Issuer's initial public offering on October 27, 2010, each share of Series B Convertible Preferred Stock (the &quot;Series B Shares&quot;), plus accrued dividends, automatically converted into shares of common stock of the Issuer in accordance with the terms of the Issuer's Third Amended and Restated Certificate of Incorporation. Each Series B Share converted into 0.61027657931 basis of common stock.</footnote>
        <footnote id="F5">The outstanding principal and accrued and unpaid interest on these Convertible Notes was automatically converted into shares of Common Stock upon the closing of the Issuer's initial public offering at $7.60 per share, which is equal to 80% of the Issuer's initial public offering price per share.</footnote>
        <footnote id="F6">These securities are owned directly by ABPIIIKG.</footnote>
        <footnote id="F7">These securities are owned directly by AEBPIII.</footnote>
        <footnote id="F8">The Series A Shares were convertible at any time, at the holder's election, and automatically upon consummation of the Issuer's initial public offering and had no expiration date.</footnote>
        <footnote id="F9">The Series B Shares were convertible at any time, at the holder's election, and automatically upon consummation of the Issuer's initial public offering and had no expiration date.</footnote>
        <footnote id="F10">The Convertible Notes were issued on September 2, 2008, December 11, 2008, July 2, 2009, January 28, 2010, June 14, 2010, August 13, 2010 and October 1, 2010.  Any outstanding principal amount and accrued but unpaid interest thereon was automatically convertible into shares of capital stock of the Issuer upon the consummation of specified sale transactions involving the securities of the Issuer, including an initial public offering of the Issuer's common stock meeting certain conditions.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>By Alta BioPharma Management Partners III, LLC
/s/ Jean Deleage, Director</signatureName>
        <signatureDate>2010-10-27</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Jean Deleage, Director</signatureName>
        <signatureDate>2010-10-27</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>by Alta BioPharma Management Partners III, LLC  /s/ Jean Deleage, Director</signatureName>
        <signatureDate>2010-10-27</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Jean Deleage, Manager</signatureName>
        <signatureDate>2010-10-27</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Jean Deleage</signatureName>
        <signatureDate>2010-10-27</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Farah Champsi</signatureName>
        <signatureDate>2010-10-27</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Edward Penhoet</signatureName>
        <signatureDate>2010-10-27</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Edward Hurwitz</signatureName>
        <signatureDate>2010-10-27</signatureDate>
    </ownerSignature>
</ownershipDocument>
