Prebiotics, in particular the chicory derived beta(2-1) fructans, have been shown to exert cancer protective effects in animal models. The present study was carried out to determine the effects of two chicory fructans--oligofructose (RaftiloseP95; average degree of polymerization DP = 4) and long chain inulin (RaftilineHP; average DP = 25), on apoptosis and bacterial metabolism associated with carcinogenesis. Eighteen rats were fed a stock diet for one week. Three groups of six animals were then fed one of three diets: basal, basal with oligofructose (5%w/w) or basal with long chain inulin (5%w/w), for a three week period. All animals were then dosed with 1,2-dimethylhydrazine and killed 24 h later. The mean number of apoptotic cells per crypt was significantly higher in the colon of rats fed oligofructose (P = 0.049) and long chain inulin (P = 0.017) as compared to those fed the basal diet alone. This suggests that oligofructose as well as the long chain inulin exert protective effects at an early stage in the onset of cancer, as the supplements were effective soon after the carcinogen insult. Comparison of the apoptotic indices between the two oligosaccharide diets showed no significant difference even though the mean apoptotic index was higher in animals fed long chain inulin. For all animals, apoptosis was significantly higher in the distal colon as compared to the proximal colon (P = 0.0002) however no significant site specific effect of diet occurred. There were no significant dietary effects on bacterial enzyme activities or ammonia concentration despite a trend towards increased colonic beta-glucosidase and reduced ammonia concentration during the oligosaccharide diets. This is the first time that a significant effect of chicory fructans on apoptosis has been shown and the results contribute to the growing evidence that chicory fructans may have cancer preventing properties.