Indium tin oxide (ITO) substrates have been modified by alkanethiol and fatty acid self-assembled monolayers (SAMs). The SAMs were grown by dipping the cleaned surface into either a pure alkanethiol or a fatty acid dissolved in various solvents. They were characterized through contact angle, X-ray photoelectron (XPS) and infrared absorption-reflection spectroscopy (IRRAS). Their density and structural organization was found to greatly depend on the cleaning treatment of the ITO surface, the length of the alkyl chain, and, in the case of fatty acids, the concentration of the solution. XPS measurements brought evidence for the fact that, in the case of alkanethiols, the grafting mechanism was through the formation of ionic or covalent bonds involving thiolates. The most prominent result of this comparative study is that thiol-based SAMs are more strongly attached to the ITO substrate and better organized than fatty acids, which we attribute to the fact that the reaction of the ITO surface with fatty acids is more reversible than that with thiols.