A non-isothermal, two-phase model for a polymer electrolyte fuel cell (PEFC) is presented, analyzed, and solved numerically under three different thermal, and two hydrodynamic, modeling assumptions; the consequences of these are then discussed in terms of thermal and water management and cell performance. The study is motivated by recent experimental results that suggest the presence of previously unreported, and thus unmodeled, thermal contact resistances between the components of PEFCs and the discrepancy in the value for the capillary pressure that is used by different authors when modeling the two-phase flow in PEFCs. For the three different thermal assumptions (assuming effective heat conductivities, isothermal flow, and interfacial and bulk conductivites), liquid saturations of around 10% are obtained at the cathode active layer for <mml:math display="inline"><mml:mn>1000</mml:mn><mml:mspace width="0.3em"></mml:mspace><mml:mi>mA</mml:mi><mml:mspace width="0.3em"></mml:mspace><mml:msup><mml:mi>cm</mml:mi><mml:mrow><mml:mo>−</mml:mo><mml:mn>2</mml:mn></mml:mrow></mml:msup></mml:math>1000mAcm−2 and a cell voltage of 0.6 V. When lowering the capillary pressure (hydrodynamic assumption), liquid saturations of almost 30% and locally up to 100% are observed at the active layer of the cathode. At this current density and voltage, temperature differences across the cell of around 9°C are predicted. In addition, the effect of varying clamping pressure within the framework of the model is touched upon. The benefits of the scaling analysis conducted here, to predict correctly, prior to numerical computations, important characteristic cell performance quantities such as current density and temperature drop are also highlighted.