A method for the separation of atropine enantiomers, D- and L-hyoscyamine by capillary electrophoresis (CE) has been developed and validated. The advantages of the CE method compared with polarimetry include smaller amounts of analytes and a lower limit of detection of the unwanted enantiomer. Moreover, the present method enables a baseline separation of the analytes and tropic acid, one of the typical impurities of atropine. The developed enantioseparation of atropine was performed using a commercially available sulfated beta-cyclodextrin and was validated for the determination of L-hyoscyamine in atropine as well as for the enantiomeric purity of L-hyoscyamine.