In this work, we examined the possibility of improving ion-exchange adsorbent performance by nanoscale structuring of ligands into clusters of fixed size rather than a random distribution of individual charges. The calcium-depleted form of the protein alpha-lactalbumin, which displays a cluster of acidic amino acid residues, showed enhanced adsorption affinity and capacity on clustered-charge pentalysinamide and pentaargininamide adsorbents as compared to single-charge lysinamide and argininamide adsorbents of matched total charge. Two differently charge-clustered mutants of rat microsomal cytochrome b(5), E11Q and E44Q, with the same total charge also were well differentiated by clustered-charge adsorbents. Thus, an organized rather than random distribution of charges may produce adsorbents with higher capacity and selectivity, especially for biomolecules with inherent charge clustering.