An affinity capillary electrophoresis method was developed for simultaneous separation ofaspartate and glutamate enantiomers fluorescently tagged with 5-(4,6-dichloro-s-triazin-2-ylamino) fluorescein. Several experimental parameters such as chiral selector, buffer concentration and pH, organic modifier were evaluated. It was proved that the inclusion complex between human serum albumin and sodium cholate, the adding order and concentration of methanol were the critical parameters. Under optimal conditions, baseline separations of these enantiomers were simultaneously achieved. The method was successfully applied to monitoring of the studied compounds in human urine.