The extraction of alpha-Lactalbumin (alpha-La) and beta-Lactoglobulin (beta-Lg) from whey have been carried out in the Aqueous Two Phase System (ATPS) composed of PEG 1000 - tri sodium citrate. The suitable conditions for the simultaneous partitioning of alpha-La into the top phase and beta-Lg in bottom phases was identified using the pure alpha-La and beta-Lg. Maximum partition coefficient (k) of 16.67 was achieved for alpha-La at the system condition of 28% (w/w) PEG 1000-14% (w/w) tri sodium citrate at pH 8 and 40 degrees C, whereas in this condition k of beta-Lg is 0.27. 30% (w/w) whey loaded to this system yielded the maximum recovery of alpha-La and beta-Lg.