Purification of PEG-protein conjugates by countercurrent distribution (CCD) in aqueous two-phase systems is reported. By using CCD in 19.36% PEG 3400/14.68% potassium phosphate, we can separate PEG-lysozyme conjugates, which contains an average number of 1.14 PEG per lysozyme, into three peaks with 55 number of transfers. Further analysis of the samples reveals that these three peaks mainly represent unmodified lysozyme, (PEG)1-lysozyme and (PEG)2-lysozyme.