The primary and secondary current distribution study indicates the geometry of a thin electrolyte in a proton exchange membrane (PEM) fuel cell has a direct relation to the measured electrode polarization, thus making the positioning of the reference electrode and ohmic compensation critical. The different kinetic overpotentials on the electrodes can also affect the potential distribution and therefore affect the measurement accuracy. The measurement error can be significant for the fuel cell system with different kinetic overpotentials and with electrode misalignment. The measurement error for both hydrogen and direct methanol fuel cells (DMFC) has been analyzed over the current density region with no mass transfer effects. By using two reference electrodes, the measurement error can be substantially decreased for both anode and cathode measurement in a direct methanol fuel cell, and for the cathode measurement in a hydrogen/air fuel cell. (C) 2003 Elsevier Ltd. All rights reserved.