Electrochemical impedance spectroscopy (EIS) was used to investigate the influence of several parameters on the performance of PEMFC. The applied frequency was in the range of 50 mHz-10 kHz. The experiment was designed by using a 2k factorial design to identify the effects of various parameters including cell voltage, flow rates of gaseous fuels and cell temperature at the saturated humidification in anode and 60% relative humidity cathode. The results indicated that the cell temperature, cell voltage and interactions of cell voltage, flow rate of H2 and O2 had a significant effect on the cell performance. In addition, the flow rate of O2 had a strong effect on the ohmic resistance and the charge transfer resistance in the system. Models describing the relationship between previous parameters and ohmic resistance, charge transfer resistance and capacitance were also developed.