Isomalto-oligosaccharides (IMO) with ¿(1¿6) and ¿(1¿4) glucosidic linkages are produced by enzymatic conversion of starch. Isomalto-oligosaccharides are partially digested in the intestine. It was the aim of this study to investigate IMO metabolism by lactobacilli and bifidobacteria and to determine the effect of IMO diet on intestinal microbiota in a rodent model and a rodent model for inflammatory bowel disease (IBD). Different strains of bifidobacteria and lactobacilli were assessed for carbohydrates metabolism in vitro. Isomalto-oligosaccharides selectively stimulated lactobacilli in rats compared to those on control or inulin diet. The potential health benefit of IMO was evaluated in a rodent model for IBD and compared to fructo-oligosaccharides (FOS) or control diet. The Lactobacillus group and bifidobacteria numbers were increased significantly in the fecal samples of rats fed IMO or FOS diet respectively. IMO and FOS diets showed a unique effect on intestinal microbiota. Inflammation was significantly decreased in the rats fed IMO or FOS diet compared to the rats fed control diet.