Hydrophilic interaction chromatography (HILIC) was employed to separate the co-eluted flavonoids from licorice extract under RP-HPLC mode. HILIC separations were carried out with the Atalantis HILIC Silica column and the CD-based column. The co-eluted flavonoids were well retained and separated on the two HILIC columns under HILIC mode. Similar results were obtained in the separation of another isoflavones sample, from kudzu extract under HILIC mode.