We describe an electrochemical deprotection method as a novel access for the site-selective immobilization of biomolecules using cyclic voltammetry, electrochemical quartz crystal microbalance, and grazing angle Fourier transform infrared spectroscopy. The hydroquinone monoester of thioctic acid and 12,12‘-dithiobis(dodecanoic acid hydroquinone monoester) were introduced as electrochemically removable protecting groups for ω-carboxylic acids of self-assembled monolayers (SAMs) on gold. The electrochemical deprotection method was found to provide very quantitative, rapid, and mild generation of specific binding sites. We additionally show that the resulting acid SAMs provide effective and selective surfaces for immobilizing oligodeoxynucleotides using radioimaging experiments and surface plasmon resonance spectroscopy.