Pore network simulations are performed to study water transport in gas diffusion layers (GDLs) of polymer electrolyte membrane fuel cells (PEMFCs). The transport and equilibrium properties are shown to be scale dependent in a thin system like a GDL. A distinguishing feature of such a thin system is the lack of length scale separation between the system size and the size of the representative elementary volume (REV) over which are supposed to be defined the macroscopic properties within the framework of the continuum approach to porous media. Owing to the lack of length scale separation, two-phase flow traditional continuum models are expected to offer poor predictions of water distribution in a GDL This is illustrated through comparisons with results from the pore network model. The influence of inlet boundary conditions on invasion patterns is studied and shown to affect greatly the saturation profiles. The effects of GDL differential compression and partial coverage of outlet surface are also investigated. (C) 2009 Elsevier B.V. All rights reserved.