﻿<?xml version="1.0" encoding="utf-8"?>
<InstanceReport xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
  <Version>2.2.0.7</Version>
  <hasSegments>false</hasSegments>
  <ReportName>Basis of Presentation</ReportName>
  <ReportLongName>006010 - Disclosure - Basis of Presentation</ReportLongName>
  <DisplayLabelColumn>true</DisplayLabelColumn>
  <ShowElementNames>false</ShowElementNames>
  <RoundingOption />
  <HasEmbeddedReports>false</HasEmbeddedReports>
  <Columns>
    <Column>
      <LabelColumn>false</LabelColumn>
      <Id>1</Id>
      <Labels>
        <Label Id="1" Label="3 Months Ended" />
        <Label Id="2" Label="Sep. 30, 2010" />
      </Labels>
      <CurrencyCode>USD</CurrencyCode>
      <FootnoteIndexer />
      <hasSegments>false</hasSegments>
      <hasScenarios>false</hasScenarios>
      <Segments />
      <Scenarios />
      <Units>
        <Unit>
          <UnitID>u000</UnitID>
          <UnitType>Standard</UnitType>
          <StandardMeasure>
            <MeasureSchema>http://www.xbrl.org/2003/iso4217</MeasureSchema>
            <MeasureValue>USD</MeasureValue>
            <MeasureNamespace>iso4217</MeasureNamespace>
          </StandardMeasure>
          <Scale>0</Scale>
        </Unit>
        <Unit>
          <UnitID>u002</UnitID>
          <UnitType>Divide</UnitType>
          <NumeratorMeasure>
            <MeasureSchema>http://www.xbrl.org/2003/iso4217</MeasureSchema>
            <MeasureValue>USD</MeasureValue>
            <MeasureNamespace>iso4217</MeasureNamespace>
          </NumeratorMeasure>
          <DenominatorMeasure>
            <MeasureSchema>http://www.xbrl.org/2003/instance</MeasureSchema>
            <MeasureValue>shares</MeasureValue>
            <MeasureNamespace>xbrli</MeasureNamespace>
          </DenominatorMeasure>
          <Scale>0</Scale>
        </Unit>
        <Unit>
          <UnitID>u001</UnitID>
          <UnitType>Standard</UnitType>
          <StandardMeasure>
            <MeasureSchema>http://www.xbrl.org/2003/instance</MeasureSchema>
            <MeasureValue>shares</MeasureValue>
            <MeasureNamespace>xbrli</MeasureNamespace>
          </StandardMeasure>
          <Scale>0</Scale>
        </Unit>
      </Units>
      <CurrencySymbol>$</CurrencySymbol>
    </Column>
  </Columns>
  <Rows>
    <Row>
      <Id>2</Id>
      <Label>Notes to the Financial Statements [Abstract]</Label>
      <Level>0</Level>
      <ElementName>epay_NotesToFinancialStatementsAbstract</ElementName>
      <ElementPrefix>epay</ElementPrefix>
      <IsBaseElement>false</IsBaseElement>
      <BalanceType>na</BalanceType>
      <PeriodType>duration</PeriodType>
      <ShortDefinition>No definition available.</ShortDefinition>
      <IsReportTitle>false</IsReportTitle>
      <IsSegmentTitle>false</IsSegmentTitle>
      <IsSubReportEnd>false</IsSubReportEnd>
      <IsCalendarTitle>false</IsCalendarTitle>
      <IsTuple>false</IsTuple>
      <IsAbstractGroupTitle>true</IsAbstractGroupTitle>
      <IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow>
      <IsEquityAdjustmentRow>false</IsEquityAdjustmentRow>
      <IsBeginningBalance>false</IsBeginningBalance>
      <IsEndingBalance>false</IsEndingBalance>
      <IsReverseSign>false</IsReverseSign>
      <PreferredLabelRole />
      <IsEPS>false</IsEPS>
      <FootnoteIndexer />
      <Cells>
        <Cell>
          <Id>1</Id>
          <ShowCurrencySymbol>false</ShowCurrencySymbol>
          <IsNumeric>false</IsNumeric>
          <IsRatio>false</IsRatio>
          <DisplayZeroAsNone>false</DisplayZeroAsNone>
          <NumericAmount>0</NumericAmount>
          <RoundedNumericAmount>0</RoundedNumericAmount>
          <NonNumbericText />
          <NonNumericTextHeader />
          <FootnoteIndexer />
          <hasSegments>false</hasSegments>
          <hasScenarios>false</hasScenarios>
          <DisplayDateInUSFormat>false</DisplayDateInUSFormat>
        </Cell>
      </Cells>
      <OriginalInstanceReportColumns />
      <ElementDataType>xbrli:stringItemType</ElementDataType>
      <SimpleDataType>string</SimpleDataType>
      <ElementDefenition>No definition available.</ElementDefenition>
      <IsTotalLabel>false</IsTotalLabel>
    </Row>
    <Row>
      <Id>3</Id>
      <Label>Basis of Presentation</Label>
      <Level>1</Level>
      <ElementName>us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock</ElementName>
      <ElementPrefix>us-gaap</ElementPrefix>
      <IsBaseElement>true</IsBaseElement>
      <BalanceType>na</BalanceType>
      <PeriodType>duration</PeriodType>
      <ShortDefinition>No definition available.</ShortDefinition>
      <IsReportTitle>false</IsReportTitle>
      <IsSegmentTitle>false</IsSegmentTitle>
      <IsSubReportEnd>false</IsSubReportEnd>
      <IsCalendarTitle>false</IsCalendarTitle>
      <IsTuple>false</IsTuple>
      <IsAbstractGroupTitle>false</IsAbstractGroupTitle>
      <IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow>
      <IsEquityAdjustmentRow>false</IsEquityAdjustmentRow>
      <IsBeginningBalance>false</IsBeginningBalance>
      <IsEndingBalance>false</IsEndingBalance>
      <IsReverseSign>false</IsReverseSign>
      <PreferredLabelRole>terselabel</PreferredLabelRole>
      <IsEPS>false</IsEPS>
      <FootnoteIndexer />
      <Cells>
        <Cell>
          <Id>1</Id>
          <ShowCurrencySymbol>false</ShowCurrencySymbol>
          <IsNumeric>false</IsNumeric>
          <IsRatio>false</IsRatio>
          <DisplayZeroAsNone>false</DisplayZeroAsNone>
          <NumericAmount>0</NumericAmount>
          <RoundedNumericAmount>0</RoundedNumericAmount>
          <NonNumbericText>&lt;div style="DISPLAY: block; MARGIN-LEFT: 0pt; TEXT-INDENT: 0pt; MARGIN-RIGHT: 0pt" align="left"&gt;&lt;font style="DISPLAY: inline; FONT-WEIGHT: bold; FONT-SIZE: 10pt; FONT-FAMILY: Times New Roman"&gt;Note 1&amp;#8212;Basis of Presentation&lt;/font&gt;&lt;/div&gt;&lt;div style="DISPLAY: block; MARGIN-LEFT: 0pt; TEXT-INDENT: 0pt; MARGIN-RIGHT: 0pt" align="justify"&gt;&amp;#160;&lt;/div&gt;&lt;div style="DISPLAY: block; MARGIN-LEFT: 0pt; TEXT-INDENT: 27pt; MARGIN-RIGHT: 0pt" align="left"&gt;&lt;font style="DISPLAY: inline; FONT-SIZE: 10pt; FONT-FAMILY: Times New Roman"&gt;The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, they do not include all of the information and footnotes required by accounting principles generally accepted in the United States for complete financial statements. In the opinion of management, all adjustments (consisting of normal recurring accruals and adjustments) considered necessary for a fair presentation of the interim financial information have been included. Operating results for the three months ended September 30, 2010 are not necessarily indicative of the results that may be expected for any other interim period or for the fiscal year ending June&amp;#160;30, 2011. For further information, refer to the financial statements and footnotes included in the Annual Report on Form 10-K for Bottomline Technologies (de), Inc. (the Company) as filed with the Securities and Exchange Commission (SEC) on September&amp;#160;10, 2010.&lt;/font&gt;&lt;/div&gt;&lt;div style="DISPLAY: block; MARGIN-LEFT: 0pt; TEXT-INDENT: 0pt; MARGIN-RIGHT: 0pt" align="justify"&gt;&amp;#160;&lt;/div&gt;&lt;div style="DISPLAY: block; MARGIN-LEFT: 0pt; TEXT-INDENT: 27pt; MARGIN-RIGHT: 0pt" align="left"&gt;&lt;font style="DISPLAY: inline; FONT-SIZE: 10pt; FONT-FAMILY: Times New Roman"&gt;Certain prior period amounts related to stock compensation expense have been reclassified to conform to the current year presentation.&lt;/font&gt;&lt;/div&gt;</NonNumbericText>
          <NonNumericTextHeader>Note 1&amp;#8212;Basis of Presentation&amp;#160;The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with accounting</NonNumericTextHeader>
          <FootnoteIndexer />
          <hasSegments>false</hasSegments>
          <hasScenarios>false</hasScenarios>
          <DisplayDateInUSFormat>false</DisplayDateInUSFormat>
        </Cell>
      </Cells>
      <OriginalInstanceReportColumns />
      <ElementDataType>us-types:textBlockItemType</ElementDataType>
      <SimpleDataType>textblock</SimpleDataType>
      <ElementDefenition>Description containing the entire organization, consolidation and basis of presentation of financial statements disclosure. May be provided in more than one note to the financial statements, as long as users are provided with an understanding of (1) the significant judgments and assumptions made by an enterprise in determining whether it must consolidate a VIE and/or disclose information about its involvement with a VIE, (2) the nature of restrictions on a consolidated VIE's assets reported by an enterprise in its statement of financial position, including the carrying amounts of such assets, (3) the nature of, and changes in, the risks associated with an enterprise's involvement with the VIE, and (4) how an enterprise's involvement with the VIE affects the enterprise's financial position, financial performance, and cash flows.  Describes procedure if disclosures are provided in more than one note to the financial statements.</ElementDefenition>
      <ElementReferences>Reference 1: http://www.xbrl.org/2003/role/presentationRef
 -Publisher FASB
 -Name FASB Staff Position (FSP)
 -Number FAS140-4 and FIN46(R)-8
 -Paragraph 8, C1, C7

Reference 2: http://www.xbrl.org/2003/role/presentationRef
 -Publisher AICPA
 -Name Accounting Research Bulletin (ARB)
 -Number 51
 -Paragraph 2-6

Reference 3: http://www.xbrl.org/2003/role/presentationRef
 -Publisher AICPA
 -Name Statement of Position (SOP)
 -Number 94-6
 -Paragraph 10

Reference 4: http://www.xbrl.org/2003/role/presentationRef
 -Publisher FASB
 -Name FASB Interpretation (FIN)
 -Number 46R
 -Paragraph 4, 14, 15

</ElementReferences>
      <IsTotalLabel>false</IsTotalLabel>
    </Row>
  </Rows>
  <Footnotes />
  <NumberOfCols>1</NumberOfCols>
  <NumberOfRows>2</NumberOfRows>
  <HasScenarios>false</HasScenarios>
  <MonetaryRoundingLevel>UnKnown</MonetaryRoundingLevel>
  <SharesRoundingLevel>UnKnown</SharesRoundingLevel>
  <PerShareRoundingLevel>UnKnown</PerShareRoundingLevel>
  <HasPureData>false</HasPureData>
  <SharesShouldBeRounded>true</SharesShouldBeRounded>
</InstanceReport>
