The performance of proton exchange membrane fuel cells (PEMFCs) with various isotropic and anisotropic permeabilities of the gas diffusion layer (GDL) was investigated using computational fluid dynamics analysis. A three-dimensional, non-isothermal model was employed with a single straight channel; both humidification and phase transportation were included in the model. The total water and thermal management for systems operating at high current densities was obtained. The results showed that the cell performance deteriorated for low isotropic permeability of the GDL. Water removal from the cathode GDL was significantly reduced in systems with low isotropic permeability or anisotropic systems with low permeabilities in both the in-plane and through-plane directions. Moreover, both the in-plane and through-plane permeabilities were found to affect water and thermal management in PEMFCs, especially in the low permeability ranges. Variations in GDL permeability had a greater influence on ohmic losses than on cathode overpotentials because the former losses depend on water and thermal management. In addition, the results showed that water and thermal management was good in systems in which the permeability in at least one direction (in-plane or through-plane) was high, whereas systems with low permeability in both the in-plane and through-plane directions exhibited poor water and thermal management. However, heat removal in PEMFCs was negatively affected by low permeability, leading to higher temperatures in the cell. The present numerical results suggested that modeling with isotropic permeability conditions may overpredict the cell performance, and inaccurately predict the water and thermal management in PEMFCs. (C) 2008 International Association for Hydrogen Energy. Published by Elsevier Ltd. All rights reserved.