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Water management is one of the key factors to ensure high performance, cold start and durability of polymer electrolyte fuel cells (PEFCs), and it is important to understand the behavior of liquid water in PEFCs. X-ray computed tomography (X-ray CT) imaging and the two-phase lattice Boltzmann method (two-phase LBM) are applied to analyze the mechanism of water transport in the gas diffusion layers (GDLs) and the gas channels in generating PEFCs. The results of the two-phase LBM are compared with those of X-ray CT imaging, and are found to agree qualitatively in that water is discharged along the hydrophilic channel wall and accumulated in the GDL, especially under the rib. The effects of the wettability of the GDLs, and of the gas channels, the diameter of the carbon fibers, and the porosity of the GDLs on water discharge from the GDLs and gas channels are also investigated.