Copolymers of acrylamide and styrene with two distinct structures were synthesized to study the effect of polymer structure on protein partitioning in two-phase aqueous systems. Micellar copolymerization was used to prepare a multiblock copolymer, while homogeneous copolymerization was used to prepare a random copolymer, both with the same composition and molecular weight. Phase behavior studies of the copolymers with poly(ethylene glycol) in water showed little difference in the phase boundaries. However, the partitioning of bovine serum albumin between the two aqueous phases was sensitive to the polymer structure. A molecular picture is proposed for the interactions between the protein and block copolymers. The effect of pH on the protein partition is analyzed in terms of the hydrophobic interactions, and the polymer and protein partitioning was correlated using a model based on the Flory-Huggins theory.