The aim of the study was to compare the effect of two types of fructans characterised by a different degree of polymerization (long-chain inulin and short-chain fructooligosaccharides [FOS]), added as single dietary components on the activity of selected bacterial enzymes in the faeces and the cecal digesta, the antioxidant status and the serum lipid profile in laboratory rats. Twenty four male Wistar rats were randomly divided into three groups and for 4 weeks were fed a control casein and two experimental diets supplemented with fructooligosaccharides and inulin at a level of 7.5% of diet (C, FOS and IN groups, respectively). The inulin addition caused a significant decrease in faecal pH value throughout the study (pH measurements were taken after day 7, 14, 21 and 28 of feeding), whereas the FOS-diet significantly decreased pH of fresh faeces only after 3 weeks of the study (p<0.05 vs. the control). Both experimental diets beneficially diminished the activity of faecal β-glucosidase and β-glucuronidase as compared to the control animals. The decreased activity of bacterial β-glucosidase and increased activity of β-galactosidase in the caecal digesta was noted only in the case of dietary FOS. The lowest concentrations of TBARS in the liver, kidneys and serum were observed in the IN group (p<0.05 vs. the control), however the FOS diet also effectively reduced concentration of TBARS in the liver tissue and the serum. The dietary inulin significantly decreased the serum glucose level and increased the percentage of HDL-cholesterol in total cholesterol (vs. C and FOS groups). The results obtained demonstrate that the consumption of diet supplemented with inulin seems to be more health promoting and elicits more beneficial changes in microflora activity, lipid metabolism and antioxidant status in rats than that enriched with short-chain fructooligosaccharides.