Recent studies have shown that the chromatographic separation of mixtures of monosaccharides and disaccharides may be improved by employing Y zeolites, a procedure which holds promise in the separation of oligosaccharides. In the present study, a column packed with zeolite was employed to study the separation of fructooligosaccharides (FOS). FOS were produced by an enzyme isolated from Rhodotorula sp., which produces GF2 (kestose), GF3 (nystose) and GF4 (frutofuranosyl nystose). The identification and quantification of the sugars were carried out by ion exchange chromatography with pulsed amperometric detection (HPAEC-PAD). The separation of fructooligosaccharides was carried out using a fixed bed column packed with Ba2+-exchange Y zeolites. The effects of temperature (40-50 degrees C), injected volume per bed volume (2.55-7.64%), superficial velocity (0.1-0.15 cm min(-1)) and eluent composition (40-60% ethanol) were investigated using a fractionary factorial design with separation efficiency as the response. The results showed that the most favorable conditions for the separation of the oligosaccharide-glucose mixture were 60% ethanol as eluent, temperature of 50 degrees C, superficial velocity of 0.1 cm min(-1) and 2.55% injection volume per bed volume of injection mixture, using two columns in series. The values for separation efficiency were 0.60 for oligosaccharide-glucose, 1.00 for oligosaccharide-fructose, 0.22 for oligosaccharide-sucrose, 0.43 for glucose-fructose, 0.82 for glucose-sucrose and 1.23 for fructose-sucrose.