We developed a novel computational method to investigate the influences of the microstructure of the polymer electrolyte fuel cell cathode catalyst layer on the overpotential characteristic toward its optimization. Three-dimensional cathode catalyst layer models were constructed by applying three-dimensional porous structure simulator and developed simulator was used to study the overpotential characteristics. Our results showed that the overpotential decreased as decrease of the standard deviation of the ionomer thickness distribution due to the increase of number of active sites. (C) 2008 Elsevier B.V. All rights reserved.