A comprehensive non-isothermal, three-dimensional computational model of a polymer electrolyte membrane (PEM) fuel cell has been developed. The model incorporates a complete cell with both the membrane-electrode-assembly (NI-EA) and the gas distribution flow channels. With the exception of phase change, the model accounts for all major transport phenomena. The model is implemented into a computational fluid dynamics code, and simulations are presented with an emphasis on the physical insight and fundamental understanding afforded by the detailed three-dimensional distributions of reactant concentrations, current densities, temperature and water fluxes. The results show that significant temperature gradients exist within the cell, with temperature differences of several degrees K within the MEA. The three-dimensional nature of the transport is particularly pronounced under the collector plates land area and has a major impact on the current distribution and predicted Limiting current density.