This study was carried out to purify hypocholesterolemic peptides from whey protein hydrolysates. Whey protein was hydrolyzed by trypsin, and then concentrated by ultrafiltration. Hydrolysates were purified with Gel Filtration Chromatography. The elution mobile phase,pH value and the concentration of mobile phase was selected for optimization. Detection methods in vitro was carried out to obtain the faction with the highest inhibition activity of cholesterol micellar solubility. The calibration curve between logarithm of protein molecular weights and appearance time was investigated. The results showed that the optimal eluent was sodium phosphate solution, the calibration curve of gel filtration chromatography was obtained, and the fraction of eluted at time 71 min had the highest hypocholesterolemic activity which was57.48%, molecular weight distribution as 2 000~4 700 u.