A non-isothermal, two-phase model is applied to a two-dimensional model of gas diffusion layer (GDL) to study the heat and mass transport in the in-plane direction (i.e. channel-to-land) and in the through-plane direction (i.e. catalyst layer-to-channel). For the first time, the anisotropy in the GDL thermal conductivity is taken into account, and found to be an important factor governing the temperature distribution in the GDL. Results predicted by our model show that the maximum temperature difference in the GDL is strongly affected by the GDL anisotropy. A temperature difference of up to 5°C is predicted, and a significant effect of temperature distribution on the water transport and distribution is observed. In addition, the latent heat effects due to condensation/evaporation of water on the temperature and water distributions are also analyzed and found to strongly affect the two-phase transport. copyright The Electrochemical Society.