Cationic porphyrins have a wide variety of uses including those as nucleic acid binding and cleaving agents, as potential pharmacological agents, as electron donor/acceptors in intramolecular electron transfer processes and as analytical reagents. Herein, we report the separation of cationic porphyrins by capillary electrophoresis on fused silica in phosphate buffer at pH 2-5. The porphyrins studied in this work were synthesized from alkylation of the parent tetrapyridylporphyrin (TPyP) to give various pyridinium porphyrins. For example, methylation of TPyP gives a mixture of the mono-, cis-di-, trans-di-, tri- and tetramethylated porphyrins [e.g., 5,10,15,20-tetrakis(N-methyl-4-pyridiniumyl)-21H,23H-p orphyrin, TMPyP(4)]. Capillary electrophoresis on a synthetic mixture showed separation of four of these compounds. Mixtures after alkylation with iodopropionic acid and bromopropylamine were also separated. The cis-di- and trimethylated TMPyP derivatives were separated on a small preparative scale by centrifugal partition chromatography. Capillary electrophoresis was also used to separate metallo TMPyP(4) complexes including those of cobalt, copper, iron, manganese, palladium, tin, vanadium and zinc. The conformational isomers (atropisomers) of 5,10,15,20-tetrakis(N-methyl-2-pyridiniumyl)-21H,23H-p orphyrin, TMPyP(2), were also separated. Net charge, molecular mass and molecular shape all contribute to the differential retention of cationic porphyrins under capillary electrophoresis conditions. Additional factors affecting the separations, including aggregation and protonation of the porphyrins, were probed by evaluating the separation of TMPyP(4) and its butyl and octyl analogs as a function of solution conditions. Cationic porphyrins are difficult to separate using traditional chromatographic methods; capillary electrophoresis and centrifugal partition chromatography provide excellent new techniques for separation of this class of compounds.