Fully coupled simulations of two-phase transport in Polymer Electrolyte Fuel Cells (PEFCs) and heat transfer in coolant channels are performed in order to investigate the effects of cooling channel configuration on the distributions of temperature and water within PEFCs. When a practical coolant flow rate is applied to large-scale cells for automotive applications, a significant coolant temperature rise is expected from the coolant inlet to the outlet, particularly under high current density operations, creating a significant cell temperature gradient along the flow direction as well. Consequently, a two-phase water profile resulting from evaporation-condensation processes inside PEFCs is also strongly influenced by the cell temperature gradient from the hot coolant inlet toward the cold coolant outlet regions, demonstrating that both temperature and liquid saturation strongly depend on the thermal gradient along the coolant flow path.