A homologous series of three cycloinulooligosaccharides were separated on the -cyclodextrin and on the silica based strong cation exchange columns using high organic content aqueous solvents. The elution order on the cyclodextrin column was from a low degree of polymerization (DP) to high DP of oligosaccharides, whereas the elution order on the cation exchange column was mixed and determined by both the metal cations on the stationary phases and the organic solvent in the mobile phases. In comparison, -, - and -cyclodextrin were also separated using the same or similar mobile phases on these columns. With no exception, the elution order was from - to -cyclodextrins.