The objective of this experiment was to determine whether supplementation with fructooligosaccharides (FOS) and (or) Lactobacillus acidophilus (LAC) affected bowel function and fermentative end-product concentrations in feces of healthy humans. Subjects (n = 68) were enrolled in a randomized, double-blind, placebo-controlled, parallel study design. After a 4-wk baseline period, subjects consumed one of the following treatments twice daily for 4 wk: 1) 3 g sucrose + 80 mg cornstarch; 2) 3 g FOS + 80 mg cornstarch; 3) 3 g sucrose + 1 x 10(9) colony-forming units (cfu) LAC; or 4) 3 g FOS + 1 x 10(9) cfu LAC. Subjects completed 7-d bowel function forms and 3-d dietary records before collection of fresh stool samples at wk 4, 6 and 8. Statistical analyses were performed on differences from baseline using the General Linear Models procedure of SAS. Fructooligosaccharides decreased fecal ammonia (P = 0.07) and isovalerate (P = 0.12) concentrations at wk 6. At wk 8, FOS tended (P = 0.11) to increase fecal putrescine concentrations. Lactobacillus decreased fecal organic matter percentage at wk 6 (P < 0.05) and 8 (P = 0.07). At wk 6 and 8, LAC increased (P < 0.05) fecal 2-methylindole, total indole, and total indole and phenol concentrations. At wk 8, LAC decreased fecal agmatine (P = 0.08) and phenylethylamine (P < 0.05) concentrations. In conclusion, FOS and LAC modified several metabolites associated with gut health, with FOS tending to be beneficial (decreased fecal protein catabolites) and LAC being negative (increased fecal protein catabolites).