A microemulsion electrokinetic chromatography method was used to separate arctiin and arctigenin in Fructus Arctii and its herbal preparations. The separation of arctiin and arctigenin was performed using a 1-butanol-SDS-ethyl acetate-water microemulsion in 10mM sodium tetraborate buffer. The analytes were baseline-resolved within 4 min. In the concentration range 5-500 microg/mL, the calibration curves reveal linear relationships between the peak area for each analyte and its concentration (correlation coefficients: 0.9993 for arctiin and 0.9998 for arctigenin). The method was applied to the analysis of arctiin and arctigenin in herbal preparations, and the recoveries were 98.7-103.1% for arctiin and 97.6-103.2% for arctigenin, respectively.