A numerical study of the 3-D characteristics of electroosmotic injection and migration of sample species in microchip capillary electrophoresis systems is reported. In particular, the effect of a non-rectangular cross section commonly found in isotropically-etched microchannels is thoroughly investigated through 3-D numerical simulations. A non-rectangular cross section resulted in a vertically non-uniform sample plug during the loading stage. Conventional 2-D simulation approach can result in up to 40% errors in the calculation of injection qualities. It was also found that the 2-D simulation using a proper channel width has a good agreement with the 3-D simulation data.