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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2016-06-14</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000827809</rptOwnerCik>
            <rptOwnerName>QLT INC/BC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>887 GREAT NORTHERN WAY,</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 250</rptOwnerStreet2>
            <rptOwnerCity>VANCOUVER</rptOwnerCity>
            <rptOwnerState>A1</rptOwnerState>
            <rptOwnerZipCode>V5T 4T5</rptOwnerZipCode>
            <rptOwnerStateDescription>BRITISH COLUMBIA, CANADA</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock, par value $0.001 per share</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnotes</value>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">QLT Inc. (&quot;QLT&quot;) may be deemed to have beneficial ownership of 6,659,291 shares of common stock, par value $0.001 per share of the Issuer (the &quot;Shares&quot;) held in the aggregate by Broadfin Healthcare Master Fund, Ltd. (&quot;Broadfin&quot;), Sarissa Capital Domestic Fund L.P. (&quot;Sarissa Capital Domestic&quot;) and Sarissa Capital Offshore Master Fund LP (&quot;Sarissa Capital Offshore&quot; and, together with Sarissa Capital Domestic, &quot;Sarissa Capital&quot;) (each of the foregoing, a &quot;Shareholder&quot; and together, the &quot;Shareholders&quot;) as a result of entering into voting agreements (the &quot;Voting Agreements&quot;) dated as of June 14, 2016 with each of Broadfin and Sarissa Capital.</footnote>
        <footnote id="F2">Pursuant to the Voting Agreements, each Shareholder agreed during the term of its Voting Agreement to, among other things, (i) vote its Shares in favor of the adoption of the Merger Agreement (as defined below) and approval of the Merger (as defined below) and the other transactions contemplated in the Merger Agreement and (ii) not sell or otherwise transfer its Shares prior to consummation of the Merger. Neither the filing of this Form 3 nor any of its contents shall be deemed to constitute an admission by QLT that it is the beneficial owner of the Shares referred to herein and such beneficial ownership is expressly denied.</footnote>
        <footnote id="F3">On June 14, 2016, QLT entered into an Agreement and Plan of Merger (the &quot;Merger Agreement&quot;) by and among the Issuer, QLT and Isotope Acquisition Corp., a Delaware corporation and wholly owned indirect subsidiary of QLT (&quot;MergerCo&quot;).  Subject to the terms and conditions of the Merger Agreement, MergerCo will merge with and into the Issuer (the &quot;Merger&quot;), with the Issuer surviving the Merger as a wholly owned indirect subsidiary of QLT.</footnote>
        <footnote id="F4">QLT does not have any pecuniary interest in any of the Shares.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Glen Ibbott</signatureName>
        <signatureDate>2016-06-23</signatureDate>
    </ownerSignature>
</ownershipDocument>
