Probiotic usage has become popular with both medical practitioners and the community in general; patients commonly seek advice regarding what, if any, such preparation would be useful for their own diseases. Since such advice should be evidence-based, identified randomized clinical trials (RCTs) for a number of gastrointestinal conditions were reviewed; the data were organized by individual probiotic genera/species. Only trials in adults were considered. Most of the identified RCTs were small and low-quality, so any conclusions to be drawn will be limited at least by methodologic problems. Using the GRADE system to consider the reliability of the evidence generated from these RCTs, it did appear that the use of fecal microbial transplantation to treat recurrent Clostridium difficile infection is well justified. Given the methodologic issues, there was moderately good evidence for preventing antibiotic-associated diarrhea with Lactobacillus, Bifidobacterium, Streptococcus, or Saccharomyces boulardii and for using Lactobacillus, Bifidobacterium, or Saccharomyces as adjunct therapy in the treatment of Helicobacter pylori. There were other conditions for which some supportive evidence was available. These conditions include VSL#3 for maintaining remissions in patients with pouchitis or treating active ulcerative colitis (UC), fecal microbial transplantation for treating active UC, Bifidobacterium for treating patients with UC in remission, Lactobacillus in patients with painful diverticulosis, a variety of probiotics (Lactobacillus, Bifidobacterium, Streptococcus, or VSL#3) in patients with minimal hepatic encephalopathy, and providing synbiotics to patients postoperatively after liver transplantation. Unfortunately, other limitations in the evidence made it very likely that future research will have an effect on the estimated benefit; these interventions cannot yet be recommended for routine use.