The influence of the side chain and the backbone segment length on the shape of the hydrophilic clusters in an ionomer with sulfonate-terminated side chains is investigated by molecular dynamics computer simulations. Different ionomer architectures, ranging from Nafion-like molecules to ionomer structures with extremely long side chains and backbone segments, are analyzed. It is shown that the size and the sulfonate population of hydrophilic clusters are differently affected by the variation of the backbone length in homologous membranes. Although the clusters swell when the backbone length is increased, they contain fewer head groups, and the average sulfonate-sulfonate separation in these swollen clusters becomes larger. An increase in the equivalent weight (EW) of homologous membranes thus hinders proton transport through hydrophilic channels. We also have shown that larger sulfonate clusters are formed in modified membranes with longer side chains. Compared to the case of membranes with shorter side chains but the same EW, those with longer side chains have a higher proton diffusivity. (C) 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 368-376, 2011