A multiplexed capillary electrophoresis system with cooling sufficient to prevent overheating during chiral separation. The system includes a thermally insulated enclosure enclosing a bundle of capillary tubes, a light source and photodetector. A heat transfer system is provided for cooling closely spaced portions and spread apart portions of the capillary tubes to an extent sufficient to prevent overheating of the tubes and contents thereof due to the heat generated during chiral separation.