This study investigated the inhibitory effects of soy isoflavones and fructooligosaccharide (FOS) on colon carcinogenesis. Sprague-Dawley male rats were injected with 1,2-dimethylhydrazine (DMH) and given experimental diets that contained 0%, 3%, 6%, or 9% FOS with or without soy isoflavones (1,000 mg/kg of diet). After 12 weeks, colonic aberrant crypt foci (ACF) formation, cyclooxygenase-2 (COX-2) expression, and fecal bile acid profiles were determined. The numbers of ACF, the numbers of ACF containing four or more crypts per focus of colonic mucosa, and the levels of COX-2 protein in the colonic epithelial tissues were significantly decreased in a dose-dependent manner in the FOS-fed, DMH-treated rats (P < .001), as compared to the DMH-treated control rats. Soy isoflavones significantly decreased the number of ACF with four or more aberrant crypts per focus (P < .001) and the amount of COX-2 protein (P < .01), independently of the effect of the oligosaccharide. The highest suppression of ACF formation was obtained with soy isoflavones combined with >or=6% FOS. No significant relationship was found between the dosage of FOS or soy isoflavones and the concentration of fecal secondary bile acid. We conclude that the combination of FOS and soy isoflavones inhibits colonic ACF formation and reduces COX-2 expression in DMH-treated rats.