A three-dimensional, gas-liquid two-phase flow and transport model has been developed and utilized to simulate the multi-dimensional, multi-phase flow and transport phenomena in both the anode and cathode sides in a proton exchange membrane (PEM) fuel cell and the cell performance with different influencing operational and geometric parameters. The simulations are presented with an emphasis on the physical insight and fundamental understanding afforded by the detailed distributions of velocity vector, oxygen concentration, water vapor concentration, liquid water concentration, water content in the PEM, net water flux per proton flux, local current density, and overpotential. Cell performances with different influencing factors are also presented and discussed. The comparison of the model prediction and experimental data shows a good agreement. Copyright (C) 2007 John Wiley & Sons, Ltd.