The purpose of this work is to numerically investigate the effects of non-uniform compression of the gas diffusion layer (GDL) and GDL intrusion into a channel due to the channel/rib structure of the flow-field plate. The focus is placed on accurately predicting two-phase transport between the compressed GDL near the ribs and uncompressed GDL near the channels, and its associated effects on cell performance. In this paper, a GDL compression model is newly developed and incorporated into a comprehensive three-dimensional, two-phase PEFC model developed earlier. To assess solely the effects of GDL compression and intrusion, the new fuel cell model is applied to a simple single-straight channel fuel cell geometry. Numerical simulations with different levels of GDL compression and intrusion are carried out and simulation results reveal that the effects of GDL compression and intrusion considerably increase the non-uniformity, particularly, the in-plane gradient in liquid saturation, oxygen concentration, membrane water content, and current density profiles that in turn results in significant ohmic and concentration polarizations. The present three-dimensional GDL compression model yields realistic species profiles and cell performance that help to identify the optimal MEA, gasket, and flow channel designs in PEFCs. Copyright (C) 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.