Over the last 20 years, self-assembled monolayers (SAMs), particularly those with alkyl chains, have been extensively studied by modifying the terminal group present at the air/SAM interface. Less well known are the effects which incorporation of a functional group within the middle of the chains might have on the overall monolayer structure and properties. We have used IRS, XPS and NEXAFS to examine the structure and characteristics of mid-chain ester functionalized alkanethiols, SH(CH2)10CO2(CH2)4CH3, SH(CH2)10CO2(CH2)9CH3, SH(CH2)15CO2(CH2)4CH3 and SH(CH2)5CO2(CH2)9CH3 on Au{111}. The embedded functional group leads to a model “stratified layer” type system with the chain below the functional group exhibiting different orientation and conformational order then the upper chain. XPS measurements show that the electrical dipole moment of the ester group affects the photoemission workfunction of the two chains differently, relevant to the phenomena arising in devices such as organic electroluminescent devices and organic field-effect transistors.