The quantitative effects of polyethylene glycol (PEG) 6000 and tripotassium phosphate on protopectinase partition in the aqueous two-phase systems were investigated using response surface methodology. With an increase in PEG 6000 less than about 3.6 g protopectinase partition increased and decreased later beyond about 4.75 g. Furthermore, protopectinase partition improved continually and reached the maximum with the increase of K3PO4 at the range of about 1.40 to 1.70 g, the statistic analysis showed that the effect of PEG (P < 0.0089) had significant effects on protopectinase partition, but the effects of the tripotassium phosphate (P < 0.9475) and the interaction of PEG 6000 and tripotassium phosphate (P < 0.2712) were not significant at the significance level of 0.05. The experimental values were shown to be in good agreement with predicted values since the correlation coefficient was 0.9410. At the optimal partition condition (4.14 g PEG 6000 and 1.71 g tripotassium phosphate in 10 ml two-phase systems), the maximum of protopectinase activity was 17.27 U/ml, which is about 2.27 folds than the other one. Key words: Central composite design (CCD), two-phase systems, polyethylene glycol/tripotassium phosphate, protopectinase partition.