This work aimed to study the partition of cheese whey proteins α-lactoalbumin and β-lactoglobulin using aqueous two-phase system by applying the cloud point extraction technique. The cloud point temperatures were determined under different concentrations of copolymer and salt. The system providing the best protein separation conditions was 20 mass% of copolymer PE61 and potassium phosphate salt solution of 100 mM, at pH 7. The protein α-lactoalbumin remained preferentially in the aqueous phase and the β-lactoglobulin was transferred to the copolymer phase.