In aqueous two-phase systems, such as PEO/pullulan and PEO/dextran systems, partitioning of linear and cyclic oligosaccharides was investigated. The alpha 1-4 linked linear oligosaccharides, such as glucose, maltose, maltotriose, maltotetraose, maltopentaose, maltohexaose, and maltoheptaose were partitioned more to the bottom polysaccharide-rich phase than to the top PEG-rich phase. The partition coefficient, K (the ratio of the concentration of oligosaccharide in the polysaccharide-rich phase to that in the PEO-rich phase), increased with an increase in the glucose units in the oligosaccharide. The extent of the partition of the oligosaccharides was affected by the structure of polysaccharide employed in the two-phase system. Compared with the PEO/pullulan system, the PEO/dextran system showed a higher partition selectivity for the linear oligosaccharides. The structural characteristics of dextran with branched skeleton should be more suitable for multipoint interactions with the linear oligosaccharides, however, more cyclodextrin (CD) was always found in the PEG phase than in the polysaccharide phase. The partition coefficient sequence of the cyclodextrins to the PEG-rich top phase was beta-CD > alpha-CD > gamma-CD. The partitioning of more beta-CD to the PEO phase may be due to better incorporation of the PEG chain into the beta-CD cavity.