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A high-speed capillary electrophoresis (HSCE) system for multiple samples was developed based on a short capillary and an automated multiwell plate sample introduction system.Twenty samples of FITC-labeled amino acids were sequentially separated with the present system within 6 min.The HSCE system consisted of a short capillary, and a commercial multiwell plate fixed vertically on a x-y-z translational stage under control of a computer program.The spontaneous injection method was used to achieve picoliter-scale sample injection from different sample wells.Under the optimized conditions, a 40-μm-long sample plug (corresponding to 78-pL plug volume) was obtained in a 50-μm i.d.capillary, which ensured both the high separation speed and high separation efficiency with a short separation length.