A complete three-dimensional and single phase CFD model for a different geometry of proton exchange membrane (PEM) fuel cell is used to investigate the effect of using different connections between bipolar plate and gas diffusion layer on the performances, current density and gas concentration. The proposed model is a full cell model, which includes all the parts of the PEM fuel cell, flow channels, gas diffusion electrodes, catalyst layers and the membrane. Coupled transport and electrochemical kinetics equations are solved in a single domain; therefore no interfacial boundary condition is required at the internal boundaries between cell components. This computational fluid dynamics code is used as the direct problem solver, which is used to simulate the three-dimensional mass, momentum and species transport phenomena as well as the electron- and proton-transfer process taking place in a PEMFC that cannot be investigated experimentally. The results show that the predicted polarization curves by using this model are in good agreement with the experimental results. Also the results show that by increasing the number of connection between GDL and bipolar plate the performance of the fuel cell enhances. (C) 2010 Elsevier B.V. All rights reserved.