A complete three-dimensional and single phase model for proton exchange membrane (PEM) fuel cells was used to investigate the effect of using different channels geometry on the performances, current density and gas concentration. The proposed model was 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 were solved in a single domain; therefore no interfacial boundary condition was required at the internal boundaries between cell components. This computational fluid dynamics code was employed as the direct problem solver, which was used to simulate the three-dimensional mass, momentum, energy and species transport phenomena as well as the electron- and proton-transfer process taking place in a PEMFC. The results showed that the predicted polarization curves by using this model were in good agreement with the experimental results and a high performance was observed by using circle geometry for the channels of anode and cathode sides. Also, the results showed that the performance of the fuel cell improved when a rectangular channel was used.