In this study, numerical simulation has been carried out for the heat transfer and temperature distribution in the cathode of polymer electrolyte membrane fuel cells along with the multi-phase and multi-species transport under the steady-state condition. The commercial software, COMSOL Multiphysics, is used to solve the conservation equations for momentum, mass, species, charge and energy numerically. The conservation equations are applied to the solid, liquid and vapor phases in the bipolar plate and gas diffusion (GDL) and catalyst layers of a two-dimensional cross section of the cathode. The catalyst layer is assumed to be a finite domain and the water production in the catalyst layer is considered to be in the liquid form. The temperature distribution in the cathode is simulated and then the effects of the relative humidity of the air stream, the permeability of the cathode and the flow channel shoulder to channel width ratio are investigated. It is shown that the highest temperature change, both in the in-plane and across-the-plane directions, occurs in the GDL, while the highest temperature is reached in the catalyst layer. The distribution of temperature in the bipolar plate is shown to be relatively uniform due to the high thermal conductivity of the plate. A decrease in the inlet relative humidity of the air stream results in the decrease of the maximum temperature due to the absorption of heat during the evaporation of liquid water in the GDL and catalyst layer. The non-uniformity of the temperature distribution, especially in the catalyst layer, is observed with the increase of the permeability of the cathode. Similarly, the decrease of the channel shoulder to channel width ratio leads to a non-uniform distribution of temperature especially under the channel areas. Copyright (C) 2009 John Wiley & Sons, Ltd.