Stool transplants, formally called fecal microbiota transplantation (FMT), are available through gastroenterology departments at major hospitals and medical centers across the United States. The procedure is currently approved only for one condition: preventing recurrent Clostridioides difficile (C. diff) infection in adults 18 and older. If you’re looking for this treatment, your path will run through a gastroenterologist, either at an academic medical center or a specialized digestive health practice.
FDA-Approved Products Available Now
Two FDA-approved microbiota products are on the market. Rebyota is administered rectally as a single dose by a healthcare provider. Vowst, approved in 2023, was the first oral option, taken as a course of capsules. Both are specifically approved to prevent C. diff from coming back after you’ve already completed a round of antibiotics for the infection.
These products replaced the older model where doctors sourced donor stool from stool banks or individual donors and administered it during a colonoscopy or via enema. That approach still exists in some settings, but the approved products have become the standard path for most patients.
Where to Find a Provider
Large academic medical centers are the most reliable places to access FMT. Cleveland Clinic, for example, offers fecal transplant through its Gastroenterology, Hepatology & Nutrition department. Mayo Clinic, Johns Hopkins, Massachusetts General Hospital, and many university-affiliated hospitals have similar programs. You can contact their gastroenterology departments directly to ask about candidacy.
Beyond major hospitals, many community gastroenterologists can prescribe the FDA-approved oral and rectal products. Since Vowst is a capsule and Rebyota is a single in-office administration, these don’t require the specialized infrastructure of a full transplant program. Your gastroenterologist can determine which product fits your situation and handle the prior authorization process with your insurance.
If you don’t already have a gastroenterologist, start with your primary care doctor. Recurrent C. diff typically involves infectious disease specialists or GI doctors, and a referral from primary care is the fastest route.
Who Qualifies for a Stool Transplant
You won’t qualify for FMT after a single C. diff infection. The treatment is reserved for recurrent cases, meaning the infection keeps coming back after antibiotic treatment. In clinical practice, most patients referred for FMT have completed three or more courses of antibiotics without the infection resolving. Some insurers may cover treatment starting at the first recurrence. UnitedHealthcare, for instance, covers Rebyota beginning at first recurrence for over 30 million of its commercial, exchange, and managed Medicaid members.
FMT is not currently approved for irritable bowel syndrome, Crohn’s disease, ulcerative colitis, or any condition other than recurrent C. diff. If you’re interested in FMT for inflammatory bowel disease, the only legal route right now is through a clinical trial (more on that below).
What the Procedure Involves
FMT can be delivered several ways: colonoscopy, enema, nasal tube into the small intestine, or oral capsules. The method depends on which product your doctor uses and your clinical situation. Research comparing capsules and enemas found that oral capsules restore gut bacteria about as effectively as enemas, with no significant difference in recovery time. Most patients today receive either Vowst capsules taken at home or Rebyota administered in a single clinic visit.
If your doctor uses the traditional colonoscopy-based approach, you’ll go through standard bowel prep the day before, and the donor material is delivered directly into the colon during the procedure. Recovery is similar to any colonoscopy, with most people resuming normal activities within a day.
Cost and Insurance Coverage
Insurance coverage for FDA-approved FMT products is broad but not automatic. Rebyota reports confirmed coverage for more than 90% of patients with commercial and government health plans. However, your out-of-pocket cost depends on your specific plan’s coinsurance rates, deductible, and whether a prior authorization is required.
Medicaid generally covers FDA-approved drugs for their labeled indication, though requirements vary by state. Some state Medicaid programs require prior authorization or follow Medicare’s coverage policies, while others set their own guidelines. UnitedHealthcare requires commercially insured patients to try Rebyota before it will cover Vowst, so the sequence of treatment may be dictated by your insurer rather than your doctor’s first choice.
If cost is a concern, ask your gastroenterologist’s office to run a benefits check before scheduling. The manufacturer of Rebyota also offers reimbursement support resources for navigating insurance.
Accessing FMT for Other Conditions
If you have ulcerative colitis or Crohn’s disease, FMT is currently restricted to clinical research settings. The evidence is promising but inconsistent. A meta-analysis of 14 randomized controlled trials found that FMT offers clinical and endoscopic benefits for ulcerative colitis, with one trial showing remission in about 30% of patients. For Crohn’s disease, a review of 12 studies reported clinical remission in 57% of adults within two to four weeks, though two randomized trials failed to meet their primary endpoints.
ClinicalTrials.gov is the best place to search for active FMT trials recruiting patients. Filter by your condition and location. Enrollment in a trial gives you access to the treatment under medical supervision at no cost, with rigorous safety monitoring.
Why DIY Stool Transplants Are Dangerous
Online communities sometimes promote at-home stool transplants using donor material from friends or family. This carries serious, potentially fatal risks. The FDA has documented cases of drug-resistant E. coli transmitted through donor stool that hadn’t been properly screened, resulting in three deaths. In one cluster, six patients developed Shiga toxin-producing E. coli infections from capsules made without adequate testing.
Proper donor screening is extensive. The FDA requires testing for dangerous strains of E. coli using sensitive molecular methods, with stool tested both before and after donation periods no more than 60 days apart. Batches are quarantined until both tests come back negative. Stool banks like OpenBiome also screen for a range of other pathogens and disclose to physicians when certain viruses haven’t been tested, so doctors can make informed decisions for vulnerable patients.
Beyond infection, documented complications of FMT include bowel perforation, bloodstream infections from gut bacteria, and fatal aspiration pneumonia when material was delivered through a nasal tube. A prospective study found that 4% of FMT recipients developed new infectious diseases within one to six months. Longer-term concerns include potential links to autoimmune conditions, inflammatory bowel disease flares, and metabolic changes. None of these risks can be managed or even detected without proper medical oversight.