A high-speed CE system for multiple samples was developed based on a short capillary and an automated sample introduction device consisting of a commercial multi-well plate and an x-y-z translation stage. The spontaneous injection method was used to achieve picoliter-scale sample injection from different sample wells. Under the optimized conditions, a 40 m-long sample plug (corresponding to 78-pL plug volume) was obtained in a 50 m id capillary, which ensured both the high separation speed and high separation efficiency. The performance of the system was demonstrated in the separation of FITC-labeled amino acids with LIF detection. Five FITC-labeled amino acids including arginine, phenylalanine, glycine, glutamic acid, and asparagine were separated within 15 s with an effective separation length of 1.5 cm. The separation efficiency ranged from 7.96 x 105/m to 1.12 x 106 /m (corresponding to 1.260.89 m plate heights). The repeatability of the peak heights calibrated with an inner standard for different sample wells was 2.4 and 2.7% (n = 20) for arginine and phenylalanine, respectively. The present system was also applied in consecutive separations of 20 different samples of FITC-labeled amino acids with a whole separation time of less than 6 min.