In this paper, the effects of microporous layer (MPL) addition and polytetrafluoroethylene (PTFE) loading of gas diffusion layers (GDLs) on the overall performance of the proton exchange membrane fuel cell have been investigated. The focus was on fuel cells that operate at relatively low current densities where the power demand is low, but the efficiency is of concern. The results show that, in the activation loss-controlled region, the performance of the fuel cell operating with moderately PTFE-treated carbon substrates is superior over that operating with coated GDLs. This is due to the addition of the MPL which lengthens the diffusion paths and significantly reduces the mass transport properties. Conversely, in the ohmic loss-controlled region, the fuel cell with coated GDLs performs better than those with carbon substrates. This is explained by the enhanced contact of the GDL with the adjacent components after the MPL addition, which outweighs the negative effects associated with the activation loss-controlled region. Also, it was found that the fuel cell performance becomes lower if the GDL is treated with a relatively high PTFE loading in either the carbon substrate (due to the decrease in the porosity of the GDL) or the MPL. Copyright (c) 2012 John Wiley & Sons, Ltd.