The present experimental study aims to determine the effect of two different gas diffusion layers in the performance of a 5-cm2 proton exchange membrane (PEM) fuel cell. The gas diffusion layers consisted of a carbon cloth gas diffusion (GDL-CT) and a non-woven carbon paper (Sigracet 25 BC, Sigracet 29, and BC Sigracet 35 BC). The effect of the GDL parameters on the fuel cell performance was evaluated by the polarization curve. Based on the polarization curve results, it was confirmed that the carbon cloth gas diffusion layer had a better performance than the non-woven carbon. Different temperatures, hydrogen flow rates and inlet pressures were tested. Images from the scanning electron microscopy were obtained to visualize the internal structure of a carbon paper GDL and a carbon cloth GDL; it was observed different surface structures between them.