A common understanding of polymer electrolyte fuel cells (PEFCs) is important to promote the development of PEFCs. This understanding is crucial because complicated phenomena such as chemical reactions, ion transport, and gas diffusion occur during the operation of PEFCs. Electrochemical impedance spectroscopy (EIS), which can separate reactions into elementary processes, is a powerful tool for the analysis of PEFCs without requiring disassembly of the cell. In this study, the effect of flooding in the cathode catalyst layer of PEFCs was analyzed by EIS using the transmission line model (TLM) to determine the distribution of catalytic reactions in the primary and secondary pores. The analysis was conducted by varying experimental conditions such as the relative humidity of the gases supplied into the anode and cathode, the flow rate, and the partial pressure of oxygen in the gas mixture supplied to the cathode channel. The EIS analysis suggests that the resistance to the catalytic reaction in the primary pores drastically increased with the current density. The results suggest that the flooding preferentially occurred in the primary pores, resulting in the reduction of active sites by generated water. The EIS method is a powerful tool for developing membrane electrode assemblies (MEAs) with effective porosity and tortuosity for gas diffusion and ionic transportation, and furthermore, it is a useful tool for judging the process of MEA preparation. (C) 2013 Elsevier Ltd. All rights reserved.