This paper describes the preparation and surface characterization of maleimide-activated silicone elastomer (PDMSMCC) followed by covalent functionalization using thiol-terminated DNA sequences (primary oligo). The stability of this attachment chemistry was demonstrated by the retention of the primary oligo through the process of hybridization with a labeled complementary DNA sequence. In these studies, the hybridized labeled DNA oligomers were detected using confocal fluorescence microscopy. We have employed a vapor deposition technique in which a plasma-treated silicone elastomer (PDMSOH) was exposed to vapors of 3-(aminopropyl)triethoxysilane (APTS) under vacuum, to yield the amine-functionalized silicone elastomer (PDMS2NH). PDMS2NH was further coupled with a heterofunctional cross-linker, sulfosuccinimidyl4-(N-maleimidomethyl)cyclohexane-1-carboxylate to obtain PDMSMCC. The surface functionalities of the elastomers were characterized using contact angle measurements and X-ray photoelectron spectroscopy. Surface-modified silicone elastomers appear to be promising substrates for use as substrates for disposable microarrays.