In this work, the effective through-plane thermal conductivities for compressed, anisotropic and heterogeneous polymer electrolyte membrane (PEM) fuel cell gas diffusion layers (GDLs) were determined analytically from representative physical GDL models, which were informed by microscale computed tomography imaging of four commercially available GDL materials. The number of fibre-to-fibre contact points and corresponding contact areas were extracted from these physical models as inputs to a thermal resistance model. It was found that the effective thermal conductivity increased with increasing GDL thickness (with bulk porosity remaining almost constant). The analytical model was employed to determine the bulk thermal conductivity as well as the thermal conductivity of the core region of the material. By isolating the core region from the bulk, a better understanding of the effect of the heterogeneous porosity profiles on the through-plane thermal conductivity was determined and discussed. Unlike the bulk thermal conductivity, the thermal conductivity of the core region was not dependent upon the material thickness. It was also found that the surface transition regions of the porosity distributions have a dominating effect over the addition of PTFE in impacting the overall thermal conductivity. (C) 2012 Elsevier B.V. All rights reserved.