The purpose of this study was to evaluate the efficacy and safety of commonly used probiotics and nutrients available for functional gastrointestinal disorders (FGID). Five different combinations of probiotics and nutrients, or placebo, were taken daily over 12 weeks. In this randomized controlled clinical trial, men and women 21 to 72 years of age with FGID symptoms of indigestion, bloating, and abdominal discomfort were assigned to one of six groups, 12 patients per group. Gastrointestinal Quality of Life Index (GIQLI) and visual analogue scale (VAS) for GI symptoms, SF-36, lactulose and mannitol test (LMT), and urine indican levels were evaluated. GIQLI, VAS scores, and LMT did not change significantly (P > 0.05). There were clinically notable improvements in two of the combination formulations. While the nonsignificant improvements in GI symptoms could suggest that combination probiotics and nutrients may be beneficial in conditions such as FGID, no conclusive evidence was found in this pilot trial. Further investigations to explore the findings are discussed.