Here, a compact high-speed CE bioanalyzer based on a short capillary has been developed. Multiple modules of picoliter scale sample injection, high-speed CE separation, sample changing, LIF detection, as well as a custom designed tablet computer for data processing, instrument controlling, and result displaying were integrated in the bioanalyzer with a total size of 23 × 17 × 19 cm (length × width × height). The high-speed CE bioanalyzer is capable of performing automated sample injection and separation for multiple samples and has been successfully applied in fast separations of amino acids, chiral amino acids, proteins and DNA fragments. For instance, baseline separation of six FITC-labeled amino acids and ultrahigh-speed separation of three amino acids could be achieved within 7 and 1 s, respectively. The separation speed and efficiency of the optimized high-speed CE system are comparable to or even better than those reported in microchip-based CE systems. We believe this bioanalyzer could provide an advanced platform for fundamental research in bioscience and clinical diagnosis, as well as in quality control for drugs, foods, and feeds.