One of the factors hindering the development of technologies that rely on the use of proton-conducting polyelectrolyte membranes is the lack of control over the membrane morphology on the nanoscale. Of particular importance is the rearrangement and clustering of acidic groups, which may seriously degrade the electrical properties. Although electron microscopy is capable of imaging the morphology of the clusters, images of unmodified membranes with sufficient quality to discriminate between different proposed cluster morphology models have not been presented. Here we show the first determination of the cluster size distribution in a model polymer electrolyte membrane from electron micrographs of individual acidic clusters. Imaging of the sulfur-rich clusters by dark-field microscopy was facilitated by the spontaneous formation of thin, cluster-containing layers on the top and bottom surfaces of free-standing films with a thickness of similar to 35 nm.