This study presents a numerical analysis of Joule heating effect on the electroosmotic flow and mass species transport, which has a direct application in the capillary electrophoresis based BioChip technology. A rigorous mathematic model for describing the Joule heating in an electroosmotic flow including the Poisson-Boltzmann equation, the modified Navier-Stokes equations and the energy equation is developed. All these equations are coupled through the temperature-dependent liquid dielectric constant, viscosity, and thermal conductivity. By numerically solving the aforementioned equations simultaneously, the double layer potential profile, the electroosmotic flow field, and the temperature distribution in a cylindrical microcapillary are computed. A systematic study is carried out to evaluate the Joule heating and its effects under the influences of the capillary radius, the buffer solution concentration, the applied electric field strength, and the heat transfer coefficient. In addition, the Joule heating effect on sample species transport in a microcapillary is also investigated by numerically solving the mass transfer equation with consideration of temperature-dependent diffusion coefficient and electrophoresis mobility. The simulations reveal that the presence of the Joule heating could have a great impact on the electroosmotic flow and mass species transport. (C) 2003 Elsevier Ltd. All rights reserved.