As one of the key components of proton-exchange membrane fuel cells, the gas-diffusion layer (GDL) that is made of carbon fibres usually exhibits strong structural anisotropy. Nevertheless, the GDL has traditionally been simplified as a homogeneous porous structure in modelling the transport of species through the GDL. In this work, a coupled electron and two-phase mass transport model for anisotropic GDLs is developed. The effects of anisotropic GDL transport properties due to the inherent anisotropic carbon fibres and caused by GDL deformations are studied. Results indicate that the inherent structural anisotropy of the GDL significantly influences the local distribution of both cathode potential and current density. Simulation results further indicate that a GDL with deformation results in an increase in the concentration polarization due to the increased mass-transfer resistance in the deformed GDL On the other hand, the ohmic polarization is found to be smaller in the deformed GDL as the result of the decreased interfacial contact resistance and electronic resistance in the GDL. This result implies that an optimum deformation needs to be achieved so that both concentration and ohmic losses can be minimized. (C) 2008 Elsevier B.V. All rights reserved.