A mathematical model incorporating both the influence of pH and solute hydrophobicity is presented to describe the partitioning of charged compounds in aqueous two-phase systems. The model is applied to the partitioning of amino acids in PEG/potassium phosphate aqueous two-phase systems in which the pH lies between 6.1 and 11.9. The model predicts the minimum in the partition coefficient of several amino acids which is observed in phase systems of intermediate pH.