Separation rates and resolutions within capillary electrophoretic (CE) systems can be enhanced when surface potentials are uniform with minimum deviations from ideal pluglike flow. Microfluidic CE devices based on poly(methyl methacrylate) (PMMA) are being developed due to the optical clarity, availability, stability, and reproducible electroosmotic flow (EOF) rates displayed by this polymer. Control of EOF in polymer-based CE systems can be achieved by surface zeta potential alteration through chemical modification. Herein, a method will be presented for the surface functionalization of PMMA with chemistry analogous to formation of trichlorosilane self-assembled monolayers on SiO2. The current method involves two separate steps. First, surface activation with water-vapor plasma introduces surface hydroxylation. Second, treatment of the plasma-treated PMMA with a substituted trichlorosilane solution forms the functional surface layer. The modified surfaces were characterized using several analytical techniques, including water contact angle, X-ray photoelectron spectroscopy, Fourier transform infrared-attenuated total reflection, secondary ion mass spectroscopy, and measurement of EOF velocities within PMMA microchannels.