The influence of the PTFE content in commercial Toray graphite paper gas diffusion layer (GDL) on the performance of a PBI-based polymer electrolyte membrane fuel cell (PEMFC) has been studied. These materials have been characterised by evaluating the porosity, pore size distribution, SEM micrographs, hydrophobicity, air permeability and electrical resistance. Fuel cell results show that the lower the Teflon content, the better the cell performance and the lower the losses when oxygen was replaced by air. These results led to non-Teflonized carbon paper to be postulated as the most suitable candidate, provided that its mechanical integrity can be maintained throughout the whole process of preparation and testing of the MEA. However, some practical problems with this type of commercial non-Teflonized carbon paper were experienced in this work and led to damage of the support. The detrimental effects are described and discussed. As conclusion, the use of a minimally PTFE-loaded (10%) carbon paper is suggested because the inclusion of this level of Teflon improved properly the mechanical properties of the carbon support and only caused a very small drop in the performance.