Capillary electrophoresis was found to give significantly higher efficiency, selectivity and speed than high-performance liquid chromatography for the separation of a mixture of flavonoid-3-O-glycosides differing in their sugar moiety. Boric acid running buffer (0.2 M, pH 10.5) was used for this electrophoretic separation. The migration order in free solution capillary electrophoresis (CE) and the selectivity of these flavonoid-3-O-glycosides can be mainly explained by in situ borate complexation of both the sugar moiety and the cis-1,2-hydroxyl groups on the flavonoid skeleton and, to a lesser extent, by the ionization of hydroxyl groups on the flavonoid skeleton due to alkaline pH conditions. The correlation of the electrophoretic mobilities with the configuration and conformation of the compounds is discussed.