A multiplexed capillary electrophoresis (CE) system equipped with 96 channels was evaluated for high-throughput screening of enantiomers of solutes of pharmaceutical interest. Using highly (DS approximately 12) sulphated alpha-, beta- and gamma-cyclodextrins under acidic conditions (pH 2.5) only 48 channels could be used because of the high conductivity of the chiral selectors. Method transfer from a single channel to a 48 channel CE system is described. Under optimised conditions, the analysis time on the multiplexed 48 channel CE system is ca. five to eight times the analysis time on the single channel CE system. The figures of merit for the multiplexed system are presented as well as performance evaluation including throughput and productivity gain. Intra-day precision (n=6) ranged from 2.0 to 16.5% and from 2.2 to 15.5% for migration time and resolution, respectively. These values increased with ca. 10% for intermediate precision.