We reported previously that feeding of fructooligosaccharides (FO) increased the apparent absorption of calcium (Ca), magnesium (Mg) and phosphorus (P) in rats. We suggested that there was an important correlation between this phenomenon and fermentation of FO in the large intestine. However, the precise mechanism remained to be characterized. Therefore, we performed a mineral-balance study to identify the segment of lumen in which FO affects mineral absorption, using cecectomized rats. Sham-operated rats and cecectomized rats were fed a control diet (without FO) or an FO-diet (containing 50 g of FO per kg of feed) for 28 days. Feeding of the FO-diet decreased the luminal pH in the cecum and colon in the sham-operated rats. In the cecectomized rats, feeding of the FO-diet also decreased the luminal pH in the colon. Thus, FO was fermented in the colon of the cecectomized rats. However, the acid composition of feces was altered by cecectomy. Feeding of the FO-diet increased the absorption of Ca and Mg in the sham-operated rats. In the cecectomized rats, the FO-diet increased the absorption of Mg but did not increase the absorption of Ca. These results suggest the mechanisms for the absorption of Ca and Mg when rats are fed an FO are different.