Four two-compartment microbial fuel cells (MFCs), equipped with the same components except for the membranes, were operated for two months within the same operation conditions, in order to evaluate the effects of the ion exchange membranes (IEM) and the hydraulic retention time (HRT). Results obtained point out that a MFC equipped with Nafion-117 achieves higher current and power densities (829 mA m(-2) and 268.37 mW m(-2), respectively) than when the same type of MFC is equipped the cationic exchange membrane Neosepta CMX or the anionic exchange membrane Neosepta AMX, despite both membranes have higher ion exchange capacities. However, no significant differences were found in the wastewater treatment capacities of the different MFCs. In addition, hydraulic retention time (HRT) was found to play an important role in the output energy generation, because low values contributes to minimize the biofouling and, hence, to produce higher current densities.