Traditional Chinese medicines (TCMs) are generally mixtures of herbal plants or extracts which comprise hundreds of different constituents with widely difference in the content and physiochemical properties. In order to analyze bioactive compounds in TCMs and control the quality, a large number of analytical tools have been developed, among which capillary electrophoresis (CE) has become a powerful technique with increasing importance. Some formats of CE, including capillary zone electrophoresis, micellar electrokinetic chromatography, non-aqueous CE and capillary electrochromatography have been widely employed for the analysis of TCMs. The general characteristics of these formats are briefly described, and their applications to the analysis of TCMs during the past five years are summarized.