<?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>123 - Disclosure - Basis of Presentation</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>eol_PE10315---13S-1-0008_STD_90_20130331_0</ContextID><EntitySchema>http://www.sec.gov/CIK</EntitySchema><EntityValue>0001069308</EntityValue><PeriodDisplayName /><PeriodType>duration</PeriodType><PeriodStartDate>2013-01-01T00:00:00</PeriodStartDate><PeriodEndDate>2013-03-31T00:00:00</PeriodEndDate><Segments /><Scenarios /></contextRef><UPS /><CurrencyCode /><OriginalCurrencyCode /></MCU><CurrencySymbol /><Labels><Label Key="CalendarSupplement" Id="0" Label="3 Months Ended" /><Label Key="Calendar" Id="1" Label="Mar. 31, 2013" /></Labels></Column></Columns><Rows><Row FlagID="0"><Id>1</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><Level>4</Level><ElementName>us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock</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="eol_PE10315---13S-1-0008_STD_90_20130331_0" UnitID=""><Id>1</Id><IsNumeric>false</IsNumeric><IsRatio>false</IsRatio><DisplayZeroAsNone>false</DisplayZeroAsNone><NumericAmount>0</NumericAmount><RoundedNumericAmount>0</RoundedNumericAmount><NonNumbericText>&lt;div&gt;
&lt;p style="MARGIN-TOP: 12px; MARGIN-BOTTOM: 0px"&gt;&lt;font style="FONT-FAMILY: Times New Roman" size="2"&gt;&lt;b&gt;Note 1. Basis of
Presentation&lt;/b&gt;&lt;/font&gt;&lt;/p&gt;
&lt;p style="MARGIN-TOP: 6px; TEXT-INDENT: 4%; MARGIN-BOTTOM: 0px"&gt;
&lt;font style="FONT-FAMILY: Times New Roman" size="2"&gt;The
accompanying interim unaudited consolidated financial statements of
Opexa Therapeutics, Inc. (&amp;#x201C;Opexa&amp;#x201D; or the
&amp;#x201C;Company&amp;#x201D;), a development stage company, have been
prepared in accordance with accounting principles generally
accepted in the United States of America and the rules of the
Securities and Exchange Commission (&amp;#x201C;SEC&amp;#x201D;) and should
be read in conjunction with the audited financial statements and
notes thereto contained in Opexa&amp;#x2019;s latest Annual Report filed
with the SEC on Form 10-K. In the opinion of management, all
adjustments, consisting of normal recurring adjustments, necessary
for a fair presentation of financial position and the results of
operations for the interim periods presented have been reflected
herein. The results of operations for interim periods are not
necessarily indicative of the results to be expected for the full
year. Notes to the financial statements that would substantially
duplicate the disclosure contained in the audited financial
statements for the most recent fiscal year as reported in Form 10-K
have been omitted.&lt;/font&gt;&lt;/p&gt;
&lt;p style="MARGIN-TOP: 12px; TEXT-INDENT: 4%; MARGIN-BOTTOM: 0px"&gt;
&lt;font style="FONT-FAMILY: Times New Roman" size="2"&gt;The
accompanying consolidated financial statements include the accounts
of Opexa and its wholly owned subsidiary, Opexa Hong Kong Limited
(&amp;#x201C;Opexa Hong Kong&amp;#x201D;). All intercompany balances and
transactions have been eliminated in the consolidation.&lt;/font&gt;&lt;/p&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 organization, consolidation and basis of presentation of financial statements disclosure.</ElementDefenition><ElementReferences>Reference 1: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 810

 -SubTopic 10

 -Section 50

 -Paragraph 8

 -URI http://asc.fasb.org/extlink&amp;oid=28200181&amp;loc=SL6228881-111685



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

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 720

 -SubTopic 15

 -URI http://asc.fasb.org/subtopic&amp;trid=2122524



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

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 205

 -SubTopic 10

 -Section 50

 -Paragraph 1

 -URI http://asc.fasb.org/extlink&amp;oid=6359566&amp;loc=d3e326-107755



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

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 235

 -SubTopic 10

 -Section 50

 -Paragraph 3

 -URI http://asc.fasb.org/extlink&amp;oid=6367646&amp;loc=d3e18780-107790



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

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 205

 -SubTopic 10

 -Section 45

 -Paragraph 3

 -URI http://asc.fasb.org/extlink&amp;oid=7668296&amp;loc=d3e288-107754



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

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 810

 -SubTopic 10

 -URI http://asc.fasb.org/subtopic&amp;trid=2197480



Reference 7: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 810

 -SubTopic 10

 -Section 50

 -Paragraph 1

 -URI http://asc.fasb.org/extlink&amp;oid=18733093&amp;loc=d3e5614-111684



Reference 8: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 915

 -SubTopic 235

 -Section 50

 -Paragraph 1

 -URI http://asc.fasb.org/extlink&amp;oid=6472506&amp;loc=d3e38932-110933



Reference 9: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 852

 -SubTopic 10

 -URI http://asc.fasb.org/subtopic&amp;trid=2209116



Reference 10: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 272

 -SubTopic 10

 -Section 50

 -Paragraph 3

 -URI http://asc.fasb.org/extlink&amp;oid=6373374&amp;loc=d3e70478-108055



Reference 11: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 275

 -SubTopic 10

 -URI http://asc.fasb.org/subtopic&amp;trid=2134480



Reference 12: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 205

 -SubTopic 10

 -URI http://asc.fasb.org/subtopic&amp;trid=2122150



</ElementReferences><IsTotalLabel>false</IsTotalLabel><UnitID>0</UnitID><Label>Basis of Presentation</Label></Row></Rows><Footnotes /><IsEquityReport>false</IsEquityReport><ReportName>Basis of Presentation</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.opexatherapeutics.com/taxonomy/role/NotesToFinancialStatementsOrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock</RoleURI><NumberOfCols>1</NumberOfCols><NumberOfRows>1</NumberOfRows></InstanceReport>
