In order to apply a numerical analysis to design an actual scale separator in polymer electrolyte fuel cell (PEFC), it is needed to enlarge the calculation size. In this study, mass transfer and flow in gas diffusion layer were calculated, and gas diffusion layer (GDL) mass transfer approximate model based on the theoretical model was developed. Next, with this model, PEFC reaction and thermal flow analysis model, which enabled us to calculate the case of an actual scale cell, was made. Furthermore, the effects of separator channel depth on output performance and current density distribution were examined with this numerical analysis. As a result, in the case of shallow channels, the oxygen transfer rate to electrode increased because of gas flow in GDL. However, current density distribution and pressure drop increased, too. This calculation model can help us to design the optimal separator shape from the comprehensive viewpoint. (c) 2005 Elsevier B.V All rights reserved.