The direct numerical simulation (DNS) method, developed for modeling the cathode catalyst layer (CL) of a polymer electrolyte fuel cell (PEFC) in Part 1, is further extended wherein the catalyst layer is described as a random three-dimensional porous structure. A random CL microstructure is obtained using a computer-generated random number with specified porosity and pore size as the input structural parameters. Some statistical features of the CL and their dependence on the porosity are identified and demonstrated. The charge and species conservation equations are solved directly on this microscopically complex structure. The results from the DNS calculation are compared with the one-dimensional macrohomogeneous predictions and the Bruggeman factor for transport property correction is evaluated, which can be used as direct input into the macroscopic fuel cell models. (c) 2005 Elsevier Ltd. All rights reserved.