Abstract The purpose of this study was to test the effects of administering bifidobacteria with either 2% fructooligosaccharide (FOS), 2% wheat bran oligosaccharide (WBOS), 2% soybean oligosaccharide (SBOS) or no added oligosaccharide (control) on cecal populations of bifidobacteria and C. perfringens, a potential pathogen and normal inhabitant of the mammalian colon, in the rat. Rats were randomly assigned to one of four treatment groups: basal diet + 1 ml daily gavage of skim milk containing 10 8 bifidobacteria, 2% FOS + bifidobacteria, 2% SBOS + bifidobacteria or 2% WBOS + bifidobacteria. The rats were fed the diets for 4 wk, after which cecal concentrations of bifidobacteria and C. perfringens were assessed. WBOS and SBOS feeding resulted in higher concentrations of bifidobacteria and C. perfringens relative to FOS-feeding or control. However, no differences in either bifidobacteria or C. perfringens were detected between control and FOS groups. Parallel to this animal study, in vitro competition experiments with bifidobacteria and C. perfringens were performed in growth media containing either glucose, FOS or WBOS as the primary carbon source. The concentrations of bifidobacteria and C. perfringens were determined at each hour for 10 h and specific growth rates (μ) were calculated. The μ for C. perfringens, co-cultured with bifidobacteria in glucose-based or WBOS-based media was significantly decreased relative to C. perfringens alone. However, no significant difference was found between the μ for C. perfringens co-cultured in FOS-based media with bifidobacteria and the C. perfringens grown alone in FOS-based media. These findings indicate that different oligosaccharides have differential effects on the populations of bifidobacteria and C. perfringens in vivo and that certain oligosaccharides may potentiate an inhibitory action of bifidobacteria against C. perfringens.