A non-isothermal stack model has been developed to analyze the effects of flow variance and temperature distribution on the performance of a polymer electrolyte membrane (PEM) fuel cell stack. The stack model consists of the flow network solver for pressure and mass flow distributions for the reactant gas streams and cooling water, and the heat transfer solver for temperature distribution among the cells in the stack, as well as the fuel cell model for individual cell performance. Temperature, pressure and concentrations of fuel and oxidant are the most important conditions for the fuel cell operation. In this work, pressure, temperature and concentration distributions are determined incorporating the individual cell performance with the minor losses in stack flow network accounted for. The results indicate that the effect of temperature is dominant on the cell voltage variance when the flow variance is small for sufficiently uniform distribution of reactant flow among the cells in the stack. Sufficient flow uniformity can be achieved by a large manifold that reduces the cell active area, or a small flow channel diameter, the latter may result in excessive pumping power for the anode and cathode gas streams. The manifold and flow channel diameters were optimized considering stack performance and reactant stream pumping power requirement. It is further shown that the flow and temperature distribution have a different influence on the stack performance, and a judicial matching of their distribution can provide the ideal uniform cell voltage distribution. An optimal combination of the flow and temperature distribution along the stack yields the optimal stack performance. (c) 2006 Elsevier B.V. All rights reserved.