A capillary electrophoresis (CE) method has been firstly used for the separation of the therapeutically important xanthones from Securidaca inappendiculata. The separation of the nine xanthones was systematically optimized with respect to pH, concentration of running buffers, addition of sulfated b-CD, applied voltage and column temperature. Baseline separation was achieved for the nine xanthones in less than 15 minutes using a background electrolyte consisting of 200 mmol/L borate (pH 9.5) and 10 mmol/L sulfated b-CD.