By using small-angle neutron scattering (SANS) reinforced by scanning electron microscopy, the fine structure of catalysts for polymer electrolyte fuel cells has been investigated. The experimental data resulting from contrast variation with mixed light and heavy water (H2O/D2O) are well described by a core-shell model with fluctuations in concentration between water and Nafion. In particular, SANS obtained with the mixed water ratio 30/70, which corresponds to a matching point between mixed water and Nafion, shows a broad scattering maximum, which is attributed to a 5 nm-thick Nafion shell on the surface of the larger carbon particles. After swelling by water, the ionomer layer absorbs water at the 17 wt% level. By changing the H2O/D2O ratio, it was further confirmed that the catalyst with the ionomer exhibits water repellence, whereas the bare catalyst without the ionomer is wetted by water. Because it is very difficult to extract more information, for instance regarding the Pt-Nafion interactions, by means of small-angle scattering, reflectometry and grazing-incidence scattering experiments with neutrons should be attempted on a model catalyst prepared on a flat substrate.