We have developed a novel method for separating macromolecules on the basis of two-phase liquid partitioning. A rotary-seal-free planetary centrifuge holds a separation column which consists of multiple partition units connected in series with transfer tubes. In the cavity of each partition unit the transfer tube extends to form a mixer which vibrates to stir the contents under an oscillating force field generated by the planetary motion of the centrifuge. Consequently, solutes locally introduced at the inlet of the column are subjected to an efficient partition process in each partition unit and separated according to their partition coefficients. The mixer tube equipped with a flexible silicone rubber joint was found to produce excellent results for partition with viscous polymer phase systems. The capability of the method was demonstrated on separation of cytochrome C and lysozyme using a PEG/K2HP04 aqueous/aqueous solvent system.