a b s t r a c tThe possibility to functionalize selectively with thiols or disulfides the surface of the gold nanoelectrodes of polycarbonate templated nanoelectrode ensembles (NEEs) is studied. It is shown that the Au nanoelectrodes can be coated by a self assembled monolayer (SAM) of thioctic acid (TA) or 2-mercaptoethanesulfonic (MES) acid. The study of the electrochemical behavior of SAM-modified NEEs by cyclic voltammetry (CV) at different solution pH, using ferrocenecarboxylate as an anionic redox probe (FcCOO − ) and (ferrocenylmethyl)trimethylammonium (FA + ) as a cationic redox probe, demonstrate that the SAM-modified nanoelectrodes are permselective, in that only cationic or neutral probes can access the SAM-coated nanoelectrode surface. CV, AFM and FTIR-ATR data indicate that proteins such as casein or bovine serum albumin, which are polyanionic at pH 7, adsorb on the surface of NEEs untreated with thiols, tending to block the electron transfer of the ferrocenyl redox probes. On the contrary, the pretreatment of the NEE with an anionic SAM protects the nanoelectrodes from protein fouling, allowing the detection of well shaped voltammetric patterns for the redox probe. Experimental results indicate that, in the case of MES treated NEEs, the protein is bound only onto the polycarbonate surface which surrounds the nanoelectrodes, while the tips of the gold nanoelectrodes remain protein free.