The membrane electrode assembly of a PEM fuel cell is hotter than the gas feeding plates because heat is generated within it, and the diffusion layers are thermally resistive. The temperature gradient created, which increases as a function of the current density, is useful for evacuating the water produced in vapor form. This water transport mechanism is known as the “heat pipe effect”. The temperature gradient produces a saturation vapour pressure gradient, which in turn produces a diffusive vapor flow. Mastering water management, coupled with heat management, requires knowledge of the temperature of the MEA and therefore the effective thermal resistance of the diffusion layers. In this paper, we present an original method for estimating this thermal resistance in situ, without using heat flux sensors or directly measuring the temperature of the MEA. The method requires the ability to impose a temperature gradient between the anode and cathode plates, and to perform a hot-side water balance. Thermal resistance is deduced from the coupling between heat and water transfer. Two diffusion layers widely used by the community are tested. The GDL Sigracet 22 BB (from SGL Carbon) has a lower effective thermal resistance than the GDL Freudenberg H15C14. Variations in these thermal resistances are measured as a function of the temperature gradient imposed and of the compression ratio.