In this study a new capillary electrophoresis (CE) method was developed to quantify the four major theaflavins occurring in black tea. Where aqueous based CE methods showed poor selectivity and considerable band broadening, non-aqueous CE achieved baseline separation of the theaflavins within 10 min. The effects of the organic solvent composition and background electrolyte concentration on the separation selectivity and electrophoretic mobilities were investigated. Our optimized separation solution consisted of acetonitrile-methanol-acetic acid (71:25:4, v/v) and 90 mM ammonium acetate. This method was used to analyze three black tea samples.