A new type of polymer, starch-modified by acrylamide, has been developed for application in aqueous two-phase systems (ATPS) for protein separation. Partial hydrolysis and acrylamide modification of starch to different degrees make it suitable for forming ATPS with poly(ethylene glycol) in a moderate concentration range. The potential of the polymer to form ATPS with the thermoprecipitating copolymer of 1-vinylimidazole with N-vinylcaprolactam (poly-VI/VCL) has been evaluated. The thermoprecipitation properties of poly-VI/VCL and Cu(II)-loaded poly-VI/VCL have been studied for application in metal affinity partitioning. The formation of ATPS with Cu(II)-loaded thermoprecipitating copolymer was critically achieved for poly-VI/VCL (10/90) copolymer in under-loaded metal concentrations. With the Cu(II)-loaded copolymer, poly-VI/VCL in the top phase and modified starch in the bottom phase, the ATPS formed was used for the purification of alpha-amylase inhibitor from wheat meal. The protein partitioned in the top phase and phase-separated polymer-protein complex could be precipitated by salt. The protein inhibitor was recovered with a yield of 75%.