The electrochemical behavior and the reactant transport in the porous gas diffusion layer (GDL) and catalyst layer (CL) are controlled by a large number of parameters such as porosity, permeability, conductivity, catalyst loading, and average pore size, etc. A three-dimensional polymer electrolyte membrane fuel cell model is developed. The model accounts for the mass, fluid, and thermal transport processes as well as the electrochemical reaction. Using this model, the effects of the various porous electrode design parameters including porosity, solid electronic conductivity, and thermal conductivity of cathode GDL, and the catalyst loading, average pore size of cathode CL are investigated through parametric study. The model is shown to agree well with the experimental data of some porous electrode specifications. In addition, the model shows promise as a tool for optimizing the design of fuel cells. Copyright (C) 2008 John Wiley & Sons. Ltd.