This article reports a 3-D numerical study on the effects of variation of surface and solution properties in microchannels on sample dispersion during electroosmotic migration. Zeta potential variations across and along the microchannel is found to generate a shear flow that increases the rate of dispersion of a sample plug. The electric conductivity variation due to the presence of a sample plug resulted in a complicated distortion of the sample plug due to the interaction between flow fields, electric potential, and species concentration. A study on the appropriateness of the 1-D Taylor dispersion method in microchip capillary electrophoresis modeling was also carried out.