Fourteen synthetic, strongly basic hexadeca- to octadecapeptides, which differ only in one amino acid residue, were synthesized and characterized. In order to investigate the application of capillary electrophoresis for the separation of mixtures of closely related basic peptides, seven different mixtures, which represent possible byproducts during solid-phase synthesis, were analyzed by HPLC and different techniques of capillary electrophoresis. Peaks within the mixture were identified by single peak injection or on-line CE/MS. Utilization of micellar electrokinetic capillary electrophoresis offered the separation of complex mixtures. Comparing the electrophoretic mobilities with calculated correlations, we found that the separation of peptides of this length is influenced not only by the different size and charge but also by hydrophobicity and the orientation of the charge due to different conformations.