Abstract: Capillary electrophoresis (CE) was applied to the study on enantiomeric migration order (EMO) of derivatives of 19 amino acids in separation systems containing the chiral selective reagents, β-cyclodextrin (β-CD) or vancomycin (VMC). Unitary β-CD separation systems were composed of β-CD in various concentrations in solutions buffered at pH 9.5 with borax buffer solution; and binary β-CD systems were composed of β-CD and sodium deoxytaurocholate in various concentration ratios, with pH values of 9.5. Unitary VMC separation system was composed of 2 mmol·L-1 VMC in borate buffer solution of pH 7.2. Binary VMC system was composed of 2 mmol·L-1 VMC and 2 mmol·L-1 HDB in borate buffer solution of pH 7.2. The 19 amino acids should be pre-derivatized with fluorenylmethoxycarbonylchlor and the derivatives were used for CE. It was found that different EMD′s were obtained for the enantiomers amino acids, and especially in the binary VMC system, EMO′s for the derivatives of amino acids were entirely reversed. Hence, separation of enantiomers of any target amino acid could be realized by using an appropriate chiral separation system.