This paper presents the results of an optimization study using a comprehensive three-dimensional, multi-phase, non-isothermal model of a PEM fuel cell that incorporates the significant physical processes and the key parameters affecting fuel cell performance. The model accounts for both the gas and liquid phase in the same computational domain and, thus, allows for the implementation of phase change inside the gas diffusion layers. The model includes the transport of gaseous species, liquid water, protons, energy and water dissolved in the ion conducting polymer. Water is assumed to be exchanged among three phases; liquid, vapor and dissolved, and equilibrium among these phases is assumed. The model features an algorithm that allows a more realistic representation of the local activation overpotentials, which leads to improved prediction of the local current density distribution. This model also takes into account convection and diffusion of different species in the channels as well as in the porous gas diffusion layer, heat transfer in the solids as well as in the gases and electrochemical reactions. The results showed that the present multi-phase model is capable of identifying important parameters for the wetting behavior of the gas diffusion layers and can be used to identify conditions that might lead to the onset of pore plugging, which has a detrimental effect on the fuel cell performance. This model is used to study the effects of several operating, design and material parameters on fuel cell performance. Detailed analyses of the fuel cell performance under various operating conditions have been conducted and examined. (c) 2007 Elsevier Ltd. All rights reserved.