Selective recovery of proteins by control of their surface properties is investigated by using a ligand modified aqueous two-phase system (ATPS) and polyethylene glycol (PEG) precipitation. The ligands used were nonionic surfactant (Triton and PEG-palmitate) and PEG-bound dye (Cibacron Blue and Procion Yellow). Both the partition coefficient in ATPS and the solubility in a PEG solution of Bovine Serum Albumin (BSA) increase significantly with the addition of these ligands, because the surface net hydrophobicity of BSA is increased by the binding of these hydrophobic ligands. On the other hand, these ligands have no effect on the partition behavior and solubility of Carbonic Anhydrase (CAB) and Ovalbumin (OvA), which have no binding sites to the ligands. Control of the surface properties of protein by these specific bindings of ligands can be utilized to improve the separation efficiency in ATPS and PEG precipitation. A separation process using ligand modified ATPS and PEG precipitation is developed.