A capillary electrophoresis microsystem integrated with feed-through platinum electrodes was designed and fabricated for the separation of DNA fragments. A novel glass-to-silicon bonding technology, which allows anodic bonding of a glass wafer to a silicon wafer coated with a thick dielectric film by the inclusion of a thin intermediate amorphous silicon layer, was developed and employed to construct the microsystem. Despite the existence of a thick insulating material and non-uniform topography, robust devices without fluid leakage were obtained. Electrophoretic manipulation and separation of DNA fragments after capillary pre-treatment have been demonstrated and several operational considerations are discussed. The system performance suggests that silicon-based microsystems can be advantageous and practical for the fabrication of integrated microcapillary electrophoresis devices.