Polymer electrolyte fuel cells (PEFCs) are comparatively efficient, environmental friendly, and scalable energy converts suitable to a wide range of applications. Heat transport in PEFCs is the important factor to improve PEFCs performance. Especially, heat transport characteristics of gas diffusion layers (GDLs) have strong influence on PEFCs performance. In PEFCs, GDL is contacted separator that has gas channels, which causes a pressure distribution in GDL. Therefore, inner structure of GDL and condition of contact between GDL and separator might be changed. So, teat transport characteristics of GDL will change. Even when liquid water is in GDL, its heat transport characteristics will be change. However, they haven't investigated clearly, yet. In this study, we measured thermal conductivities and thermal resistances of GDLs in the through-plane direction using steady state method, and effects of gas channel geometry and inside water distribution are discussed. We found that contact condition between GDL and separator didn't change GDL-separator thermal contact resistance per unit contact area. And when there is water retention in GDL, we found that water distribution and degree of water content inside GDL influences the thermal conductivity of GDL and GDL-separator thermal contact resistance.