<?xml version="1.0" encoding="us-ascii"?><InstanceReport xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><Version>2.4.0.8</Version><ReportLongName>111 - Disclosure - Collaborative Agreements</ReportLongName><DisplayLabelColumn>true</DisplayLabelColumn><ShowElementNames>false</ShowElementNames><RoundingOption /><HasEmbeddedReports>false</HasEmbeddedReports><Columns><Column FlagID="0"><Id>1</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><CurrencyCode /><FootnoteIndexer /><hasSegments>false</hasSegments><hasScenarios>false</hasScenarios><MCU><KeyName /><CurrencySymbol /><contextRef><ContextID>P01_01_2013To06_30_2013</ContextID><EntitySchema>http://www.sec.gov/CIK</EntitySchema><EntityValue>0000934473</EntityValue><PeriodDisplayName /><PeriodType>duration</PeriodType><PeriodStartDate>2013-01-01T00:00:00</PeriodStartDate><PeriodEndDate>2013-06-30T00:00:00</PeriodEndDate><Segments /><Scenarios /></contextRef><UPS /><CurrencyCode /><OriginalCurrencyCode /></MCU><CurrencySymbol /><Labels><Label Key="CalendarSupplement" Id="0" Label="6 Months Ended" /><Label Key="Calendar" Id="1" Label="Jun. 30, 2013" /></Labels></Column></Columns><Rows><Row FlagID="0"><Id>1</Id><IsAbstractGroupTitle>true</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><Level>1</Level><ElementName>gnvc_CollaborativeAgreementAbstract</ElementName><ElementPrefix>gnvc_</ElementPrefix><IsBaseElement>false</IsBaseElement><BalanceType>na</BalanceType><PeriodType>duration</PeriodType><IsReportTitle>false</IsReportTitle><IsSegmentTitle>false</IsSegmentTitle><IsCalendarTitle>false</IsCalendarTitle><IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow><IsEquityAdjustmentRow>false</IsEquityAdjustmentRow><IsBeginningBalance>false</IsBeginningBalance><IsEndingBalance>false</IsEndingBalance><IsReverseSign>false</IsReverseSign><FootnoteIndexer /><Cells><Cell FlagID="0" ContextID="" UnitID=""><Id>1</Id><IsNumeric>false</IsNumeric><IsRatio>false</IsRatio><DisplayZeroAsNone>false</DisplayZeroAsNone><NumericAmount>0</NumericAmount><RoundedNumericAmount>0</RoundedNumericAmount><NonNumbericText /><FootnoteIndexer /><CurrencyCode /><CurrencySymbol /><IsIndependantCurrency>false</IsIndependantCurrency><ShowCurrencySymbol>false</ShowCurrencySymbol><DisplayDateInUSFormat>false</DisplayDateInUSFormat></Cell></Cells><ElementDataType>xbrli:stringItemType</ElementDataType><SimpleDataType>string</SimpleDataType><IsTotalLabel>false</IsTotalLabel><UnitID>0</UnitID><Label>Collaborative Agreement [Abstract]</Label></Row><Row FlagID="0"><Id>2</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><Level>2</Level><ElementName>us-gaap_CollaborativeArrangementDisclosureTextBlock</ElementName><ElementPrefix>us-gaap_</ElementPrefix><IsBaseElement>true</IsBaseElement><BalanceType>na</BalanceType><PeriodType>duration</PeriodType><IsReportTitle>false</IsReportTitle><IsSegmentTitle>false</IsSegmentTitle><IsCalendarTitle>false</IsCalendarTitle><IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow><IsEquityAdjustmentRow>false</IsEquityAdjustmentRow><IsBeginningBalance>false</IsBeginningBalance><IsEndingBalance>false</IsEndingBalance><IsReverseSign>false</IsReverseSign><PreferredLabelRole>terseLabel</PreferredLabelRole><FootnoteIndexer /><Cells><Cell FlagID="0" ContextID="P01_01_2013To06_30_2013" UnitID=""><Id>1</Id><IsNumeric>false</IsNumeric><IsRatio>false</IsRatio><DisplayZeroAsNone>false</DisplayZeroAsNone><NumericAmount>0</NumericAmount><RoundedNumericAmount>0</RoundedNumericAmount><NonNumbericText>              &lt;table border="0" style="clear:both;width:100%; table-layout:fixed;"&gt;  &lt;tr&gt;  &lt;td&gt;&lt;/td&gt;  &lt;/tr&gt;  &lt;/table&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif "&gt;  &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0in 0in 0pt; FONT-SIZE: 10pt"&gt;  &lt;table style="clear:both;MARGIN-TOP: 0px; FONT: 10pt Times New Roman, Times, Serif; MARGIN-BOTTOM: 0px"   cellspacing="0" cellpadding="0"&gt;  &lt;tr style="TEXT-ALIGN: justify; VERTICAL-ALIGN: top"&gt;  &lt;td style="TEXT-ALIGN: left; WIDTH: 0.5in"&gt;  &lt;div&gt;&lt;strong&gt;(6)&lt;/strong&gt;&lt;/div&gt;  &lt;/td&gt;  &lt;td style="TEXT-ALIGN: justify"&gt;  &lt;div&gt;&lt;strong&gt;Collaborative Agreements&lt;/strong&gt;&lt;/div&gt;  &lt;/td&gt;  &lt;/tr&gt;  &lt;/table&gt;  &lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &amp;#160;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  In January 2010, we signed a research collaboration and license  agreement (the Agreement) with Novartis to discover and develop  novel treatments for hearing loss and balance disorders. Under  the&amp;#160;terms of the Agreement, we licensed the world-wide rights  to our preclinical hearing loss and balance disorders program.The  Agreement was extended in January 2012 and again in January 2013.  Under the extensions, Novartis will fund research at GenVec through  January 2014 to support the preclinical hearing loss and balance  disorders program. When the Agreement was executed in January 2010,  we&amp;#160;received a $&lt;font style=" FONT-SIZE: 10pt"&gt;5.0&lt;/font&gt;  million non-refundable upfront license fee and Novartis purchased  $&lt;font style=" FONT-SIZE: 10pt"&gt;2.0&lt;/font&gt; million of our common  stock. The common stock was recorded at fair value of $&lt;font style=" FONT-SIZE: 10pt"&gt;3.3&lt;/font&gt; million on the date of issuance.  The&amp;#160;non-refundable upfront license&amp;#160;fee was recognized  ratably over the original two-year research and collaboration term  of the Agreement. Due to the pricing agreement associated with the  sale of our common stock, revenue recognized from the  non-refundable upfront license fee&amp;#160;was $&lt;font style=" FONT-SIZE: 10pt"&gt;3.7&lt;/font&gt; million by the end of  the&amp;#160;initial Agreement, as extended, in January 2014. In  addition, we will receive funding from Novartis for a research  program focused on developing additional adenovectors for hearing  loss. No revenue from the upfront license fee was recognized during  the three months ended June 30, 2013 or 2012. There was $&lt;font  style=" FONT-SIZE: 10pt"&gt;118,000&lt;/font&gt; and $&lt;font style=" FONT-SIZE: 10pt"&gt;198,000&lt;/font&gt; of revenue recognized for  research performed under the Agreement for the three months ended  June 30, 2013 and 2012, respectively. During the six months ended  June 30, 2013 and 2012 we recognized $&lt;font style=" FONT-SIZE: 10pt"&gt;0&lt;/font&gt; and $&lt;font style=" FONT-SIZE: 10pt"&gt;78,000&lt;/font&gt;, respectively, of the upfront  payment and $&lt;font style=" FONT-SIZE: 10pt"&gt;252,000&lt;/font&gt; and  $&lt;font style=" FONT-SIZE: 10pt"&gt;429,000&lt;/font&gt;, respectively, for  research performed under the Agreement.&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &amp;#160;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  Under the Agreement, we are eligible to receive milestones payments  of up to $&lt;font style=" FONT-SIZE: 10pt"&gt;206.6&lt;/font&gt; million,  including up to $&lt;font style=" FONT-SIZE: 10pt"&gt;0.6&lt;/font&gt; million  for the achievement of preclinical development activities, up to  $&lt;font style=" FONT-SIZE: 10pt"&gt;26.0&lt;/font&gt; million for the  achievement of clinical milestones (including non-rejection of  an&amp;#160;investigational new drug with respect to a covered product,  the first patient visit in Phase I, Phase IIb, and Phase III  clinical trials), up to $&lt;font style=" FONT-SIZE: 10pt"&gt;45.0&lt;/font&gt;  million for the receipt of regulatory approvals and up to $&lt;font  style=" FONT-SIZE: 10pt"&gt;135.0&lt;/font&gt; million for sales milestones.  We have recognized $&lt;font style=" FONT-SIZE: 10pt"&gt;600,000&lt;/font&gt;  of milestone payments as a result of the successful completion of  preclinical development activities prior to 2012. There were no  milestones achieved in 2012 or during the six months ended June 30,  2013.&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &amp;#160;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  In August 2010, we signed an agreement with Novartis for the supply  of services relating to development materials in  connection&amp;#160;with the companies' collaboration on  the&amp;#160;hearing loss and balance disorders program. Under this  agreement, GenVec could receive approximately $&lt;font style=" FONT-SIZE: 10pt"&gt;13.0&lt;/font&gt; million over four years to  manufacture clinical trial material for up to two lead candidates.  During the three months ended June 30, 2013 and 2012 we recognized  $&lt;font style=" FONT-SIZE: 10pt"&gt;0.1&lt;/font&gt; million and $&lt;font  style=" FONT-SIZE: 10pt"&gt;1.0&lt;/font&gt; million, respectively, for  services performed under this agreement. During the six months  ended June 30, 2013 and 2012 we recognized $&lt;font style=" FONT-SIZE: 10pt"&gt;0.3&lt;/font&gt; million and $&lt;font style=" FONT-SIZE: 10pt"&gt;2.2&lt;/font&gt; million, respectively, for services  performed under this agreement.&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &amp;#160;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  In September 2012, we signed an agreement worth approximately  $&lt;font style=" FONT-SIZE: 10pt"&gt;3.5&lt;/font&gt; million with the U.S.  Naval Medical Logistics Command&amp;#160; to&amp;#160;support malaria  vaccine developmentefforts at the U.S. Naval Medical Research  Center (NMRC). Under the terms of the agreement, GenVec was  responsible for producing clinical supplies of its malaria vaccine,  which utilizes its novel, proprietary technology. NMRC used the  clinical material as part of its efforts&amp;#160;to assess the safety  and efficacy of these next-generation vectored vaccines using the  clinical challenge model developed by NMRC and the Walter Reed Army  Institute of Research (WRAIR) malaria vaccine programs, which now  are unified as the U.S. Military Malaria Vaccine Program (USMMVP).  Under the agreement, GenVec retains the right to commercialize this  novel technology. No revenue was recognized under this contract  during the three and six month periods ended June 30, 2013 or 2012.  See Note 9, Subsequent Event, for a description of the modification  of this agreement.&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &amp;#160;&lt;/div&gt;    &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  &lt;div style="clear:both; FONT-FAMILY:Times New Roman;FONT-SIZE: 10pt;MARGIN: 0pt 0px; FONT: 10pt Times New Roman, Times, Serif"&gt;  In April 2013, the National Institutes of Allergy and Infectious  Diseases (NIAID) of the National Institutes of Health (NIH)  announced that it will stop administering injections in its HVTN  505 clinical trial of an investigational HIV vaccine regimen  because an independent data and safety monitoring board (DSMB)  found during a scheduled interim review that the vaccine regimen  did not prevent HIV infection nor reduce viral load (the amount of  HIV in the blood) among vaccine recipients who later became  infected with HIV. The HVTN 505 trial was designed to test the  safety and efficacy of a two-part HIV vaccine regimen consisting of  one vaccine designed to prime the immune system followed by another  vaccine designed to boost the immune response. GenVec manufactured  the adenovirus vector component utilized as the boost vaccine for  this trial.&lt;/div&gt;  &lt;/div&gt;  &lt;/div&gt;        </NonNumbericText><FootnoteIndexer /><CurrencyCode /><CurrencySymbol /><IsIndependantCurrency>false</IsIndependantCurrency><ShowCurrencySymbol>false</ShowCurrencySymbol><DisplayDateInUSFormat>false</DisplayDateInUSFormat></Cell></Cells><ElementDataType>nonnum:textBlockItemType</ElementDataType><SimpleDataType>na</SimpleDataType><ElementDefenition>The entire disclosure for collaborative arrangements in which the entity is a participant, including a) information about the nature and purpose of such arrangements; b) its rights and obligations thereunder; c) the accounting policy for collaborative arrangements; and d) the income statement classification and amounts attributable to transactions arising from the collaborative arrangement between participants.</ElementDefenition><ElementReferences>Reference 1: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 808

 -SubTopic 10

 -Section 50

 -Paragraph 1

 -URI http://asc.fasb.org/extlink&amp;oid=6931272&amp;loc=SL5834143-161434



</ElementReferences><IsTotalLabel>false</IsTotalLabel><UnitID>0</UnitID><Label>Collaborative Agreements</Label></Row></Rows><Footnotes /><IsEquityReport>false</IsEquityReport><ReportName>Collaborative Agreements</ReportName><MonetaryRoundingLevel>UnKnown</MonetaryRoundingLevel><SharesRoundingLevel>UnKnown</SharesRoundingLevel><PerShareRoundingLevel>UnKnown</PerShareRoundingLevel><ExchangeRateRoundingLevel>UnKnown</ExchangeRateRoundingLevel><HasCustomUnits>true</HasCustomUnits><IsEmbedReport>false</IsEmbedReport><IsMultiCurrency>false</IsMultiCurrency><ReportType>Sheet</ReportType><RoleURI>http://www.genvc.com/role/CollaborativeAgreements</RoleURI><NumberOfCols>1</NumberOfCols><NumberOfRows>2</NumberOfRows></InstanceReport>
