In this paper the anisotropic effective thermal conductivity of the gas diffusion layer (GDL) of polymer electrolyte membrane fuel cell is determined using the two- and three-dimensional two-phase conjugate fluid-solid thermal lattice Boltzmann model. Using stochastic reconstructions of the GDL, the effective thermal conductivity is evaluated in the through-plane and in-plane directions. It is shown that the anisotropic structure of the GDL results in an anisotropic thermal conductivity, with a higher value for the in-plane thermal conductivity than the through-plane thermal conductivity. We show that the two-dimensional in-plane simulations provided reasonable estimates of the thermal conductivity at a significantly lower computational cost than the three-dimensional simulations. Adding the third dimension, however, dampens the effect of structure randomness and reduces the variance in the predicted data points. The predicted values of effective through-plane thermal conductivity from two-dimensional simulations are almost one order of magnitude smaller than those predicted from three-dimensional simulations. The fibers are better connected in the three-dimensional reconstructed structures, which create a preferential path for heat transport, and thus a higher effective thermal conductivity. The predicted values of effective thermal conductivity are in good agreement with previously reported values in the literature. (C) 2012 The Electrochemical Society. [DOI: 10.1149/2.013206jes] All rights reserved.