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

    <schemaVersion>X0203</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2010-10-21</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001197540</rptOwnerCik>
            <rptOwnerName>FISHERMAN JASON S</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>75 STATE STREET, 29TH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02109</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>13</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series A Convertible Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>3565</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series B Convertible Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1245</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Senior Subordinated Convertible Promissory Notes</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>7.60</value>
                <footnoteId id="F6"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F5"/>
            </exerciseDate>
            <expirationDate>
                <value>2011-12-31</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2286</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Reflects a 1-for-2.4417 reverse stock split effected on October 19, 2010 in connection with the Issuer's initial public offering.</footnote>
        <footnote id="F2">Shares are indirectly beneficially owned as a limited partner of Advent Partners HLS III Limited Partnership.</footnote>
        <footnote id="F3">The Series A Convertible Preferred Stock (the &quot;Series A Shares&quot;) and the Series B Convertible Preferred Stock (the &quot;Series B Shares&quot;) are convertible, in accordance with the Issuer's Third Amended and Restated Certificate of Incorporation, at any time after the issuance of such shares, at the holder's election.</footnote>
        <footnote id="F4">The Series A Shares and the Series B Shares, including all accrued and unpaid interest thereon, will convert automatically into Common Stock without payment of any additional consideration, upon the closing of the Issuer's initial public offering and do not have an expiration date.  The Series A Shares will convert on a 1-for-0.38701117412 basis and the Series B Shares will convert on a 1-for-0.61027657931 basis.</footnote>
        <footnote id="F5">Reflects $15,753,09 aggregate principal and interest amount of senior subordinated convertible promissory notes (the &quot;Convertible Notes&quot;,) dated September 2, 2008, December 11, 2008, July 2, 2009, January 28, 2010, June 14, 2010, August 13, 2010, and October 1, 2010.  The outstanding principal and accrued and unpaid interest on these Convertible Notes shall automatically be converted into shares of common stock upon the closing of the Issuer's initial public offering.</footnote>
        <footnote id="F6">The outstanding principal and accrued and unpaid interest on these Convertible Notes shall automatically be converted into shares of common stock upon the closing of the Issuer's initial public offering at $7.60 per share, 80% of the Issuer's initial public offering price per share.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Jarlyth H. Gibson, Attorney-in-Fact</signatureName>
        <signatureDate>2010-10-22</signatureDate>
    </ownerSignature>
</ownershipDocument>
