This paper proposes a three-dimensional (3D) volume of fluid (VOF) study to investigate two-phase flow in the gas diffusion layer (GDL) of proton exchange membrane (PEM) fuel cells and liquid water distribution. A stochastic model was adopted to reconstruct the 3D microstructures of Toray carbon papers and incorporate the experimentally-determined varying porosity. The VOF predictions were compared with the water profiles obtained by the X-ray tomographic microscopy (XTM) and the Leverett correlation. It was found local water profiles are similar in the sample's sub-regions under the pressure difference Delta p = 1000 Pa between the two GDL surfaces, but may vary significantly under Delta p = 6000 Pa. The water-air interfaces inside the GDL structure were presented to show water distribution and breakthrough. (C) 2018 The Electrochemical Society.