A simple and effective purification process for heat shock proteins (HSPs), in which PEG fractional precipitation was combined with an aqueous two-phase system (ATPS), was successfully developed based upon the proteins’ molecular surface properties. Both GroEL and GroES, typical HSPs from E.coli, were selectively partitioned to the PEG (top) phase of the ATPS, GroEL and GroES were selectively and stepwisely concentrated from the above PEG phase by PEG fractional precipitation, In addition, the purification of GroEL and GroES as a complex by using biospecific affinity with adenosine triphosphate (ATP) was achieved. GroEL and GroES can be purified either as individual native molecules or as a 1:1 complexed state by the control of ATP addition.