A capillary electrochromatography (CEC) method with diode-array detection has been developed for the separation of the therapeutically important anthraquinones from Rhubarb extract and commercial traditional Chinese drugs containing Rhubarb. The separation of four major anthraquinones (aloe-emodin, emodin, chrysophanol, and physcion) was optimized with respect to pH and concentration of buffers, addition of acetonitrile, applied voltage, and column temperature. Baseline separation was achieved for the four anthraquinones in less than 12 min using a background electrolyte consisting of 5 mM acetic acid (pH 4.5) with 80% acetonitrile. The possibility of CEC for the analysis of traditional Chinese medicines was discussed*.