The capillary walls of fused-silica capillary electrophoresis (CE) columns were modified with a thin film of polyaniline (PANI), providing open-tubular columns with a stable coating containing aromatic groups and amine functionalities. Fast and efficient separations were observed for small bioactive peptides under acidic conditions on PANI-coated columns. The mechanism of separation is based on hydrophobic interactions between the analytes and the polymeric matrix. Good reproducibility was observed from run-to-run. Due to the simple derivatization procedure, method flexibility, the uniformity of the coating and its stability, conjugated polymers could find practical application in capillary zone electrophoresis (CZE) separations.