The role of polymer concentration, ionic strength, and salt type on the partitioning of proteins in aqueous two-phase systems is studied both experimentally and theoretically. Polymer-induced protein-protein interactions are also considered in terms of a perturbation theory, and are shown to not significantly affect the protein partition coefficient at moderate concentrations. A thermodynamic model combining the UNIQUAC and extended Debye-Huckel equations accounts for changes in salt type and salt concentration on protein partitioning with good accuracy, and calculated protein partition coefficients are in good agreement with experimental observations. Based on this detailed thermodynamic analysis, a simple model for the protein partition coefficient is developed and is shown to be useful for correlating measurements.