Transport phenomena in the gas diffusion layer (GDL) are of vital importance for the operation of direct methanol fuel cells (DMFCs). In this work, a two-phase mass transport model is developed to investigate the effects of anisotropic characteristics of a GDL, including the inherent anisotropy, deformation, and electrical and thermal contact resistances, on the coupled species, charges and thermal transport processes in a DMFC. In this model, methanol crossover and non-equilibrium evaporation/condensation of water and methanol are considered. The multistep electrochemical mechanisms are used to obtain a detailed description of the kinetics of methanol oxidization reaction (MOR) in both the anode and cathode catalyst layers (CLs). The numerical results show that the anisotropy of the GDL has a great effect on the distribution of species concentration, overpotential, local current density, and temperature. The deformation of the GDL depresses the transport of species through the GDL, particularly methanol diffusion in anode GDL, but facilitates the transport of electron and the removal of heat. The electrical contact resistance plays an important role in determining the cell performance. (C) 2009 Elsevier B.V. All rights reserved.