PEM fuel cell assembly pressure is known to cause large strains in the gas diffusion layer (GDL), which results in significant changes in its mechanical, electrical and thermal properties. These changes affect the rates of mass, charge, and heat transport through the GDL, thus impacting fuel cell performance and lifetime. The appropriate modeling of the inhomogeneous GDL compression process associated with the repetitive channel-rib pattern is therefore essential for a detailed description of the physical-chemical processes that take place in the cell. In this context, the mechanical characterization of the GDL is of special relevance, since its microstructure based on carbon fibers has strongly nonlinear orthotropic properties. The present study describes a new finite element model which fully incorporates the nonlinear orthotropic characteristics of the GDL, thereby improving the prediction of the inhomogeneous compression effects in this key element of the cell. Among other conclusions, the numerical results show that the linear isotropic models widely reported in the literature tend to overestimate the porosity and the partial intrusion of the GDL in the channel region, and may lead to incorrect predictions in terms of interfacial contact pressure distributions. Copyright (C) 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.