A series of polyelectrolyte multilayers (PEMs) has been fabricated using polyanions and polycations that have repeat units (i) similar in structure and composition (matched), (ii) partially similar in structure and composition (semimatched), and (iii) very different in structure and composition (mismatched). The primary aim of this investigation was to determine whether the matching of the polyelectrolytes can significantly influence the permeability properties of hyperthin PEMs. While matching, per se, was not found to be a key factor in defining membrane permeability, large differences in permeability were observed (the permeances of N-2 varied by a factor of 20), which were correlated with the concentration of pendant aryl groups present, i.e., the greater the concentration of these groups, the higher the permeability. Analysis by AFM indentation measurements further revealed that high-permeability PEMs tend to be more compliant than low-permeability PEMs. These findings underscore the need for considering a broad range of polyelectrolyte combinations when optimizing a particular functional property of PEMs.