A CZE method was developed for the simultaneous determination of 15 flavonoids, including epimedin B, epimedin A, hexandraside F, epimedin C, icariin, sagittatoside B, sagittatoside A, hexandraside E, 2″-O-rhamnosyl icariside II, baohuoside VII, baohuoside I, caohuoside C, epimedoside C, baohuoside II, and kaempferol-3-O-rhamnoside, in different species of Epimedium, and the effect of stability of internal standard (IS) on quantification was also investigated. As a result, rutin was not available for use as an IS because of its unstable property in sample solution, which suggested that the stability of IS both in standards and sample solution should be considered for the analysis. Using stable daidzein as IS, the analysis was performed within 35 min by using 50 mM borax buffer containing 20% ACN as a modifier (pH 10.0), while separation voltage was 25 kV and temperature was at 30°C. The method was validated to be accurate, simple, and repeatable, and was successfully applied to the analysis of 36 samples from 17 species of Epimedium. © 2009 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.