A method for the spatially selective biofunctionalization of silicon micro- and nanostructures is reported, and results are presented for both single-crystal silicon (111) or (100) surfaces. An electroactive monolayer of hydroquinone was formed on the surface of H-terminated silicon working electrodes via an olefin reaction with UV-generated surface radicals. Molecules presenting either cyclopentadiene or a thiol group can be immobilized onto the regions where the hydroquinone has been oxidized. Molecular size and crystal orientation are evaluated as important factors that dictate the electrode stability in aqueous solution under anodic potentials. Monolayers composed of smaller molecules on (111) surfaces exhibit the highest packing density and are more effective in preventing anodic oxidation of the underlying substrate. Voltammetry, X-ray photoelectron spectroscopy, and atomic force and fluorescence microscopy are utilized to interrogate the kinetic rates of biofunctionalization, the extent of surface coverage, monolayer quality, and the spatial selectivity of the process.