Five different flavonoids in Semen Cuscutae were determined for the first time by micellar electrokinetic chromatography (MEKC) and reversed-phase high-performance liquid chromatography (RP-HPLC). MEKC was carried out on a 68.5-cm fused-silica capillary using 0.035 mol/L sodium dodecyl sulfate and 0.02 mol/L borate-phosphate (pH 7.0) containing 10% methanol as the running buffer. RP-HPLC was performed on a 12.5-cm Hypersil C18 (Agilent Technologies, Palo Alto, CA, U.S.A.) column with a 0.025-mol/L phosphate acid (A) - methanol (B) solvent gradient. Both MEKC and HPLC are rapid, simple, and efficient. The results obtained using these techniques are compared. MEKC and HPLC can be complementary to each other for the quality control of Semen Cuscutae.