A micellar electrokinetic capillary chromatographic (MEKC) method with diode-array detection is developed for the characterization of pharmacologically active flavonoids in extracts prepared from Epimedium brevicornum, E. humanense, E. coactum, and E. truncatum. The pK(a) values of icarin, epimedin B, and epimedin C are determined by spectrophotometry. Optimal separation of icarin, epimedin B and C, and eight other compounds is achieved by determining pK(a) values and by systematically optimizing electrolytic and instrumental parameters. The repeatability of analyses and the reliability of identification are evaluated by the marker technique. Calculated for relative migration times of flavonoids in the extracts, the repeatability of the analyses varies from 0.7 to 6.4% (nine replicates). For migration indices calculated with two markers, however, the repeatability almost falls below 0.5%. The distribution of the flavonoids is found to differ both qualitatively and quantitatively among the four species. The MEKC technique appears to provide a powerful tool for the identification and quality control of plant drugs and for phytotaxonomic investigations.