The present study compares a charge/hydrophobicity capillary electrophoresis (CE) approach to reversed-phase high -performance liquid chromatography (RP-HPLC) for the separation of three series of four synthetic, random coil peptide standards. Each series has peptides of the same positive charge (+1, +2 and +3 series) and length but -differing in hydrophobicity. Complete resolution of the 12 peptides was achieved via a novel CE approach: a capillary zone electrophoresis (CZE) mode effected a separation of identically charged peptides; within each charged group of peptides, the addition of perfluorinated acid anionic ion-pairing reagents allowed resolution of the peptides through a mechanism based on peptide hydrophobicity which we have termed ion-interaction (II)-CZE. The peak capacity and peptide resolution of this CE approach was superior to that of RP-HPLC and stresses an important role for CE for peptide/ proteomic applications.