Amino acids react with OPA and chiral mercaptans to give diastereomeric isoindole derivatives. The resolution of these diastereomers was investigated by micellar electrokinetic chromatography (MECC) and free solution capillary electrophoresis. MECC with SDS as micellar phase allows to separate the amino acid derivatives and to resolve the diastereomers. The separation is influenced by the amount of detergent and the organic modifier added. Capillary zone electrophoresis offers a valuable alternative to the traditional methods for amino acid analysis and enantiomer determination.