The recovery of biomolecules represents an important field of study in evolution with fundamental application in the advances of biotechnology. In this work, the study of α-lactalbumin (α-La) and β-lactoglobulin (β-Lg) partitioning was carried out using aqueous two-phase systems (formed by polymer/maltodextrin) with different synthetic polymers (polyethylene glycol_PEG, polypropylene glycol_PPG, polyvinylpyrrolidone_PVP) and different molecular weights (from 425 to 40000). The influence of the type, molecular weight and percentage of the polymer used in the system was evaluated in the partition of these proteins. The results indicated that maltodextrin may be a good substitute for dextran in the processes with aqueous two phase aqueous system and it was observed that after the process the proteins tend to remain in the maltodextrin rich phase