The pore structure of the cathode catalyst layer of proton-exchange membrane (PEM) fuel cells is a major factor influencing cell performance. The nanostructure of the catalyst layer has been probed using a novel combination of mercury porosimetry with computerized X-ray tomography (CXT), even though the nanopores were below the nominal CXT resolution. The method allows probing of the macroscopic spatial variability in the accessibility of the nanostructure. In particular, mercury entrapment within the catalyst layer showed a pronounced regular spatial patterning corresponding to the already higher X-ray absorbing regions of the fresh catalyst layer. The initial, greater X-ray absorption was due to a higher local concentration of carbon-supported platinum catalyst. This was due to segregation of ionomer away from these areas caused by the particular screen printing catalyst layer deposition method used, which both enhanced the accessibility of the origin regions and, concomitantly, reduced the accessibility of the destination regions.