Continuous counter-current column operation provides operating convenience for contacting two-phase aqueous partitioning systems for protein extraction. We discuss in detail the important parameters for designing spray, packed, plate and York-Scheibel columns for protein recovery using both polymer-polymer and polymer-salt two-phase aqueous systems. We compare the various contractors for their operating and extraction efficiency. The work also provides a step-by-step design procedure and specific recommendations for future data needs.