Aqueous and non-aqueous capillary electrophoresis (CE) systems were employed for the separation of basic and acidic polar drugs using capillary zone electrophoresis (CZE) and micellar electrokinetic chromatography (MECC) techniques. This work was performed to determine the differences in selectivity, after chemical adjustment of the media, of the separation of closely related drugs (by measurement of separation efficiency, resolution and detection) in aqueous and non-aqueous solvents. Various electrolytes were tested in aqueous and organic solvent media. The best separation in aqueous CZE was obtained in 25 mM phosphate solution at pH 7.3. In aqueous MECC, the best performance was obtained in pH 10.5 buffer containing glycine and dodecyl sulfate. Non-aqueous CE separations were performed in electrolyte mixtures containing methanol–acetonitrile, ethanol–acetonitrile and propan-2-ol–acetonitrile (50∶49, v/v) modified by ammonium acetate and water-free glacial acetic acid. Acetone was also used instead of acetonitrile in the separation media. In non-aqueous CE systems, the effect of water in the non-aqueous sample and as part of the electrolyte solution played a significant role in the separation of polar anionic drugs.