Proton exchange membranes (PEMs) are one of the most important components in microbial fuel cells (MFCs), since PEMs physically separate the anode and cathode compartments while allowing protons to transport to the cathode in order to sustain an electrical current. The Nafion 117 membrane used in this study is generally regarded as having excellent proton conductivity, though many problems for its application in MFCs remain. We investigated problems associated with Nafion including: oxygen leakage from cathode to anode, substrate loss, cation transport and accumulation rather than protons, and biofouling. It was found that Nafion was quite permeable to oxygen. The oxygen mass transfer coefficient (K-O) and the oxygen diffusion coefficient (D-O) for Nafion was estimated as K-O = 2.80 x 10(-4) cm/s and D-O = 5.35 x 10(-6) cm(2)/s, respectively when a 50 mM phosphate buffer was used as the catholyte. The MFC with distilled water instead of phosphate buffer showed similar values (K-O = 2.77 x 10(-4) cm/s, D-O = 5.27 x 10(-6) cm(2)/s), indicating that the catholyte shows no significant effects on oxygen diffusion. Nafion was also found to be-permeable to acetate, but this seems to be negligible. Cations in the anolyte, presenting in high concentration due to their supply to optimize the anodic bacterial growth condition, were rapidly transported through the Nafion membrane. They occupied negatively charged sulfonate groups of Nafion, which consequently reduced contact chance of protons due to their competition. According to energy dispersive X-ray (EDX) analysis, the relative atomic percentage of carbon (30.9%) and fluoride (59.7%), the basic backbone materials of Nafion, in used Nafion was lowered, compared to that obtained with new Nafion (C = 32.8%, F = 60.1%); whereas sodium and iron, which do not exist in new Nafion, increased by up to 1.16% and 0.24% of the atoms, respectively. This indicates that these two cation species already occupied an important fraction of the negatively charged sulfonate groups, which can cause the hindrance of proton migration. Nafion operated over a period of 50 days was contaminated with biofilm causing adverse effects on mass transport through the membrane. Bacteria growing on Nafion were much more heterogeneous compared to those observed on the anode carbon felt surface. The densest biofilm was observed in the outermost few millimeters of anode carbon felt, and the biofilm density gradually decreased with inward depth.