Patients with large bowel disease may undergo ileal pouch-anal anastomosis, in which the colon is removed and part of the distal ileum is used to construct a pelvic reservoir. Competence of the ileal pouch to ferment carbohydrates is associated with the absence of pouchitis. However, the extent to which bacterial fermentation takes place and whether it is affected by diet are unclear. We investigated fermentation of two nondigestible carbohydrates, fructooligosaccharides and resistant starch, in 15 healthy patients with an ileal pouch by using a placebo-controlled crossover design (with glucose as the placebo). Apparent fermentability of fructooligosaccharides was 83%; that of resistant starch was 46%. Resistant starch increased fecal excretion of butyrate by 69% whereas fructooligosaccharides reduced excretion of amino acid-derived isobutyrate by 94% and of isovalerate by 77%. Fructooligosaccharides also significantly increased fecal weight (651 compared with 541 g/d) and breath-hydrogen excretion (286 compared with 85 ppm x h). Bacterial fermentation of nondigestible carbohydrates in pouches takes place to an appreciable extent and in a substrate-specific manner. The relation between such fermentation and inflammation of the pouch (pouchitis) deserves study.