Effects of a perfluorosulfonate ionomer (PFSI) and of a polytetrafluoroethylene (PTFE) loaded carbon (PTFE-C) on the catalyst layer in the electrode of a polymer electrolyte fuel cell (PEFC) prepared by a new method based on the process of PFSI-colloid formation were investigated by electrochemical techniques and a mercury pore sizer. The microstructure of the catalyst layer and its effect on the PEFC performance were affected by the contents of both PFSI and PTFE-C. The catalyst layer has two distinctive pore distributions with a boundary of ca. 0.04 mu m. The volume of larger pore (secondary pore) deceased with an increase of the PFSI content and increased with an increase of the PTFE-C content. The volume of the smaller pore (primary pore) was independent of the content of both PFSI and PTFE-C. The PFSI as well as the PTFE existed only in the secondary pore. The content of PFSI affected the performance of PEFC in the whole current density range. On the other hand, the content of PTFE-C influenced it greatly at high current density due to its gas feeding faculty. in the PEFC, reaction sites were found to exist in the secondary pore coated with the macromolecule PFSI. The hydrophobic PTFE-C works to supply the reaction gas to the reaction sites covered with the PFSI in the secondary pore, and to exhaust the product water from there. The high performance of PEFC at high current density was achieved with the best mixture of the PFSI and the PTFE-C.