To perform chiral separation of three flavonoid racemates, including dihydrodaidzein, equol and alpinetin, a simple and effective method was developed by using sulfobutyl ether-beta-cyclodextrin (SBE-beta-CD) as a mobile phase additive in HPLC system. The effects of different factors on the chiral separation were investigated, including cyclodextrin (CD) types (alpha-CD, gamma-CD, beta-CD, methyl beta-CD), CD concentration (5, 10, 20 mmol/L), pH value, nature of organic solvents (methanol, ethanol, acetonitrile) and phosphate buffer concentration. The analysis was carried out on a Kromasil 100-5C18 column (250 mm x 4.6 mm, 5 microm). The mobile phase consisted of acetonitrile and 10 mmol/L SBE-beta-CD aqueous solution( containing 20 mmol/L KH2PO4, at pH 4.0 adjusted with phosphoric acid) (20: 80, v/v). The flow rate was set at 1 mL/min, the column temperature was 25 degrees C, and the UV detections of dihydrodaidzein, equol and alpinetin were carried out at 276, 280 and 290 nm, respectively. The established method was able to separate the three racemates, and the resolutions of the enantiomers (dihydrodaidzein, equol and alpinetin) were 1.8, 1.9 and 1.4, respectively. This method might be applied to separate various types of flavanoid enantiomers in chemical structure.