Cyclodxtrin homologues(CDs), produced by cyclodextrin glycosyltransferase(CGTase), were simultaneously partitioned in aqueous two-phase system(ATPS). Partition coefficients of CDs were measured in PEG/dextran systems. Phosphate, citrate, sulfate were tested as salt. ATPS of PEG/salt and PEG/dextran had the partition coefficients of the CDs, larger than unity. However, PEG/dextran system was observed better than PEG/salt as CGTase activity decreased sharply with salt concentration. Enzymatic rection occurred mainly in PEG-rich bottom phase because of the low partition coefficient of CGTase. The resulting CDs transferred to the PEG-rich top phase, obeying the diffusional partition. In the ATPS of 7% PEG(M.W.40, 000), 7mg/ml of CDs were obtained in top phase at 4.5 hours.