<?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>109 - Disclosure - Fair Value of Financial Instruments</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>0000894158</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>us-gaap_FairValueDisclosuresAbstract</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><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>Fair Value Disclosures [Abstract]</Label></Row><Row FlagID="0"><Id>2</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><Level>2</Level><ElementName>us-gaap_FairValueDisclosuresTextBlock</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>label</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;size: 8.5in 11.0in"&gt;  &lt;table style="clear:both;WIDTH: 100%; BORDER-COLLAPSE: collapse"  border="0" cellspacing="0" cellpadding="0" width="100%"&gt;  &lt;tr&gt;  &lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 1%; PADDING-RIGHT: 0in; PADDING-TOP: 0in"   valign="top" width="1%"&gt;  &lt;div style="clear:both;MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"&gt;  &amp;#160;&lt;/div&gt;  &lt;/td&gt;  &lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 1.58%; PADDING-RIGHT: 0in; PADDING-TOP: 0in"   valign="top" width="1%"&gt;  &lt;div style="clear:both;MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"&gt;  &lt;strong&gt;&lt;font style="COLOR: black"&gt;4.&lt;/font&gt;&lt;/strong&gt;&lt;/div&gt;  &lt;/td&gt;  &lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 97.42%; PADDING-RIGHT: 0in; PADDING-TOP: 0in"   valign="top" width="97%"&gt;  &lt;div style="clear:both;MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"   align="justify"&gt;&lt;strong&gt;&lt;font style="COLOR: black"&gt;&amp;#160;Fair  Value of Financial Instruments&lt;/font&gt;&lt;/strong&gt;&lt;/div&gt;  &lt;/td&gt;  &lt;/tr&gt;  &lt;/table&gt;    &lt;div style="clear:both;TEXT-INDENT: 27.5pt; MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"   align="justify"&gt;&lt;font style="COLOR: black"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;    &lt;div style="clear:both;MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"   align="justify"&gt;&lt;font style="COLOR: black"&gt;The fair value  accounting standards define fair value as the amount that would be  received to sell an asset or paid to transfer a liability in an  orderly transaction between market participants. As such, fair  value is determined based upon assumptions that market participants  would use in pricing an asset or liability. Fair value measurements  are rated on a three-tier hierarchy as follows:&lt;/font&gt;&lt;/div&gt;    &lt;div style="clear:both;TEXT-INDENT: 27.5pt; MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"   align="justify"&gt;&lt;font style="COLOR: black"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;    &lt;table style="clear:both;WIDTH: 100%; BORDER-COLLAPSE: collapse"  border="0" cellspacing="0" cellpadding="0" width="100%"&gt;  &lt;tr&gt;  &lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 3%; PADDING-RIGHT: 0in; PADDING-TOP: 0in"   valign="top" width="3%"&gt;  &lt;div style="clear:both;MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"&gt;  &lt;font style="COLOR: black"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;  &lt;/td&gt;  &lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 3%; PADDING-RIGHT: 0in; PADDING-TOP: 0in"   valign="top" width="3%"&gt;  &lt;div style="clear:both;MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"&gt;  &lt;font style="FONT-FAMILY: Symbol; COLOR: black"&gt;&amp;#8901;&lt;/font&gt;&lt;/div&gt;  &lt;/td&gt;  &lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 94.02%; PADDING-RIGHT: 0in; PADDING-TOP: 0in"   valign="top" width="94%"&gt;  &lt;div style="clear:both;MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"   align="justify"&gt;&lt;font style="COLOR: black"&gt;Level 1 inputs: Quoted  prices (unadjusted)&amp;#160;for identical assets or liabilities in  active markets;&lt;/font&gt;&lt;/div&gt;  &lt;/td&gt;  &lt;/tr&gt;  &lt;/table&gt;    &lt;div style="clear:both;TEXT-INDENT: -14.3pt; MARGIN: 0in 0in 0pt 29.7pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"   align="justify"&gt;&lt;font style="COLOR: black"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;    &lt;table style="clear:both;WIDTH: 100%; BORDER-COLLAPSE: collapse"  border="0" cellspacing="0" cellpadding="0" width="100%"&gt;  &lt;tr&gt;  &lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 3%; PADDING-RIGHT: 0in; PADDING-TOP: 0in"   valign="top" width="3%"&gt;  &lt;div style="clear:both;MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"&gt;  &lt;font style="COLOR: black"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;  &lt;/td&gt;  &lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 3%; PADDING-RIGHT: 0in; PADDING-TOP: 0in"   valign="top" width="3%"&gt;  &lt;div style="clear:both;MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"&gt;  &lt;font style="FONT-FAMILY: Symbol; COLOR: black"&gt;&amp;#8901;&lt;/font&gt;&lt;/div&gt;  &lt;/td&gt;  &lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 94.02%; PADDING-RIGHT: 0in; PADDING-TOP: 0in"   valign="top" width="94%"&gt;  &lt;div style="clear:both;MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"   align="justify"&gt;&lt;font style="COLOR: black"&gt;Level 2 inputs: Inputs,  other than quoted prices included in Level 1 that are observable  either directly or indirectly; and&lt;/font&gt;&lt;/div&gt;  &lt;/td&gt;  &lt;/tr&gt;  &lt;/table&gt;    &lt;div style="clear:both;TEXT-INDENT: -14.3pt; MARGIN: 0in 0in 0pt 29.7pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"   align="justify"&gt;&lt;font style="COLOR: black"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;    &lt;table style="clear:both;WIDTH: 100%; BORDER-COLLAPSE: collapse"  border="0" cellspacing="0" cellpadding="0" width="100%"&gt;  &lt;tr&gt;  &lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 3%; PADDING-RIGHT: 0in; PADDING-TOP: 0in"   valign="top" width="3%"&gt;  &lt;div style="clear:both;MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"&gt;  &lt;font style="COLOR: black"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;  &lt;/td&gt;  &lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 3%; PADDING-RIGHT: 0in; PADDING-TOP: 0in"   valign="top" width="3%"&gt;  &lt;div style="clear:both;MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"&gt;  &lt;font style="FONT-FAMILY: Symbol; COLOR: black"&gt;&amp;#8901;&lt;/font&gt;&lt;/div&gt;  &lt;/td&gt;  &lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 94.02%; PADDING-RIGHT: 0in; PADDING-TOP: 0in"   valign="top" width="94%"&gt;  &lt;div style="clear:both;MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"   align="justify"&gt;&lt;font style="COLOR: black"&gt;Level 3 inputs:  Unobservable inputs for which there is little or no market data,  which require the reporting entity to develop its own  assumptions.&lt;/font&gt;&lt;/div&gt;  &lt;/td&gt;  &lt;/tr&gt;  &lt;/table&gt;    &lt;div style="clear:both;TEXT-INDENT: 27.5pt; MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"   align="justify"&gt;&lt;font style="COLOR: black"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;    &lt;div style="clear:both;MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"   align="justify"&gt;&lt;font style="COLOR: black"&gt;If the inputs used to  measure fair value fall in different levels of the fair value  hierarchy, the hierarchy level is based upon the lowest level of  input that is significant to the fair value  measurement.&lt;/font&gt;&lt;/div&gt;    &lt;div style="clear:both;TEXT-INDENT: 27.5pt; MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"   align="justify"&gt;&lt;font style="COLOR: black"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;    &lt;div style="clear:both;MARGIN: 0in 0in 0pt; FONT-FAMILY: Times New Roman,serif; FONT-SIZE: 10pt"   align="justify"&gt;&lt;font style="COLOR: black"&gt;Cash and cash  equivalents include money market accounts&amp;#160;of $&lt;font style=" FONT-SIZE: 10pt"&gt;6.9&lt;/font&gt; million and $&lt;font style=" FONT-SIZE: 10pt"&gt;10.0&lt;/font&gt; million as of June 30, 2013 and  December 31, 2012, respectively, that are measured using Level 1  inputs.&lt;/font&gt;&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 the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.</ElementDefenition><ElementReferences>Reference 1: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 825

 -SubTopic 10

 -Section 50

 -Paragraph 21

 -URI http://asc.fasb.org/extlink&amp;oid=28364263&amp;loc=d3e13537-108611



Reference 2: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 825

 -SubTopic 10

 -Section 50

 -Paragraph 10

 -URI http://asc.fasb.org/extlink&amp;oid=28364263&amp;loc=d3e13433-108611



Reference 3: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 825

 -SubTopic 10

 -Section 50

 -Paragraph 28

 -URI http://asc.fasb.org/extlink&amp;oid=6957238&amp;loc=d3e14064-108612



Reference 4: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 820

 -SubTopic 10

 -Section 50

 -Paragraph 2

 -URI http://asc.fasb.org/extlink&amp;oid=25499696&amp;loc=d3e19207-110258



Reference 5: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 825

 -SubTopic 10

 -Section 50

 -Paragraph 30

 -URI http://asc.fasb.org/extlink&amp;oid=6957238&amp;loc=d3e14172-108612



Reference 6: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 825

 -SubTopic 10

 -Section 50

 -Paragraph 16

 -URI http://asc.fasb.org/extlink&amp;oid=28364263&amp;loc=d3e13504-108611



</ElementReferences><IsTotalLabel>false</IsTotalLabel><UnitID>0</UnitID><Label>Fair Value Disclosures [Text Block]</Label></Row></Rows><Footnotes /><IsEquityReport>false</IsEquityReport><ReportName>Fair Value of Financial Instruments</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.syntheticbiologics.com/role/FairValueOfFinancialInstruments</RoleURI><NumberOfCols>1</NumberOfCols><NumberOfRows>2</NumberOfRows></InstanceReport>
