The oxygen reduction reaction (ORR) in the cathode catalyst layer (CCL) of polymer electrolyte fuel cells (PEFC) is one of the major causes of performance loss during operation. In addition, the CCL is the most expensive component due to the use of a Pt catalyst. Apart from the ORR itself, the species transport to and from the reactive sites determines the performance of the PEFC. The effective transport properties of the species in the CCL depend on its nanostructure. Therefore a three-dimensional reconstruction of the CCL is required. A series of two-dimensional images was obtained from focused ion beam - scanning electron microscope (FIB-SEM) imaging and a segmentation method for the two-dimensional images has been developed. The pore size distribution (PSD) was calculated for the three-dimensional geometry. The influence of the alignment and the anisotropic pixel size on the PSD has been investigated. Pores were found in the range between 5 nm and 205 nm. Evaluation of the Knudsen number showed that gas transport in the CCL is governed by the transition flow regime. The liquid water transport can be described within continuum hydrodynamics by including suitable slip flow boundary conditions.