Fecal Transplant: What You Should Know

Medically Reviewed by Melinda Ratini, MS, DO on March 28, 2025
7 min read

A fecal transplant is a procedure that places the stool of a healthy person into the colon of someone who’s ill. Your doctor may call it bacteriotherapy.

Who needs a fecal transplant?

Doctors sometimes use a fecal transplant to treat a serious bacterial infection called C. difficile, or C. diff.

Like most infections, C. diff is usually treated with antibiotics. But in some people, the infection can come back again and again. It won’t respond to more antibiotics.

A fecal transplant is sometimes a more successful treatment for repeated C. diff than antibiotics. It often clears up the infection quickly.

How does a fecal transplant work?

It puts stool full of healthy bacteria into your colon. When you have enough good bacteria in your gut, the bad bacteria that cause disease are held in check.

Antibiotics can wipe out the bacteria that make you sick. But they may also clear out the bacteria that keep your body healthy. Without that balance, the bad bacteria can take over. They make toxins that make you sick with diarrhea and colitis.

By restoring the healthy bacteria balance in your gut, a fecal transplant can help you fight infection and feel better quickly. It may also help your body resist C. diff in the future.

Could a fecal transplant treat other diseases?

Unbalanced gut bacteria may play a role in other health problems too. 

“Other indications that have been reported for fecal transplant have been inflammatory bowel disease — that's Crohn's disease and ulcerative colitis,” says Runa Watkins, MD, an associate professor of pediatric gastroenterology at the University of Maryland School of Medicine in Baltimore. 

“There's also been some literature looking at autism spectrum disorders and microbiota, though there's no evidence-based medicine for that.” 

Doctors have also begun to test fecal transplants on people who have:

  • Cirrhosis
  • Multiple sclerosis
  • Depression
  • Obesity
  • Food allergies
  • Diabetes and diabetic neuropathy

Fecal transplants show a lot of promise as treatments for ulcerative colitis. One reason may be that people with UC often have an unhealthy mix of gut bacteria that makes it hard for them to fight off stomach infections.

In one study, people with UC received a fecal transplant that used poop from two donors mixed together. Some saw improved symptoms and lower inflammation at only one month after the transplant, and 15% of patients went into remission. That means they had no UC symptoms at all.

There is some evidence that donor “matching” can improve the chance of success for people with ulcerative colitis. A donor in good health is important, and it may help if they are close to you in age. In addition, it seems that family members often make better donors than those chosen at random. Sibling donors seem to do better than parent or child donors — possibly because they tend to be closer in age.

Scientists need to do more research to learn why fecal transplants work for some people with UC but not for others.

There are different ways doctors can perform a fecal transplant:

Colonoscopy

Doctors collect a donor’s bowel movement and mix it with saline solution, then strain it through a coffee filter. The result is a brown liquid that contains the good bacteria. The doctor injects it deep into your colon using a long, flexible tube called a colonoscope.

Upper endoscopy

An upper endoscopy uses a tube that goes through your mouth or nose and down into your stomach or small intestine. Doctors use this method if you can’t have a colonoscopy. But it’s not as successful because the bacteria from the transplant must travel through the small intestine before they reach the colon.

Enema

An enema uses a tube placed inside of your bottom (rectum) to deliver the stool. This way, the bacteria can move directly into your colon without traveling through the small intestine, which is safer and works better.

Fecal transplant pills

It isn’t as widely used, but there is a newer type of fecal transplant that comes in capsule form called Vowst. The doctor places it in your gut through a long tube that goes up your nose and down into your belly. Donated poop is screened, prepared, and frozen, then placed inside little capsules. You’ll get 15 capsules over two days. It doesn’t sound pleasant, but it works well to clear up diarrhea from recurrent C. diff.

Another approved fecal transplant that is given rectally one time is called Rebyota.

The FDA has only approved two types of fecal transplants: an enema and the pills.

Fecal transplant donors

Most stool donors are family members or friends, but they don’t have to be. You can also get frozen, screened poop transplants from stool banks.

Stool donors and their poop are carefully screened. “We want to make sure that the donor doesn't have any underlying gastrointestinal diseases or even any other immunologic conditions,” Watkins says. Donors also get blood and stool tests to check for infections or drugs that could be passed along in their poop. Stool donors can’t take antibiotics for at least a month before the transplant.

To qualify as a stool donor, you can’t have:

  • A compromised immune system
  • Inflammatory bowel disease (IBD)
  • A history of illegal drug use or drug abuse
  • Ever been in prison
  • Gotten a tattoo or body piercing 6 months before the donation
  • Traveled to areas where you might have been exposed to certain infections

Can you do fecal transplant on your own?

Should you try a do-it-yourself fecal transplant to save time or money? No.

Donated stool needs to be screened to check for traces of any bad bacteria, infections, or drugs. A do-it-yourself fecal transplant could harm the person who gets the donation. You could get a serious infection even if the stool comes from someone who doesn’t appear to be sick.

How to prepare for a fecal transplant

Two days before a fecal transplant, you’ll need to stop taking all antibiotics. If you’re having a colonoscopy, follow the bowel prep provided by your doctor. It may involve a clear liquid diet and an enema or laxative. You’ll also need bowel prep if you’re taking fecal transplant pills. A fecal transplant enema doesn’t require any special prep.

This procedure usually takes place in a hospital or doctor’s office. If you’re having a colonoscopy, you’ll get medicine to make you sleep through the whole thing. You’ll also take loperamide (Imodium) to keep you from having diarrhea. This helps you hold in the donated stool so it’s more effective.

With an enema, you’ll lie on your side on a hospital table and bring your knees to your chest. Your doctor will apply a lubricant inside your anus, and then insert a tube, which is attached to a bag with the stool. The procedure takes a few minutes.

If you’re taking fecal transplant pills, your doctor will prescribe four pills a day for three days. You’ll take the pills after finishing a course of antibiotics and prepping your bowels.

Fecal Transplant Recovery

You’ll go home or to your hospital room to rest after the transplant is finished. It’s best to take it easy for the rest of the day.

Side effects

There are possible side effects with fecal transplants. The antibiotics used with the procedure can cause diarrhea, a rash, and nausea. The transplant can cause bowel issues and nausea. But so far, research shows the effects are not typically serious and usually go away with time.

  • Fecal transplants restore healthy gut bacteria by transferring stool from a donor to your colon.
  • The procedure mainly treats recurring C. diffinfections, but it may help with other gut conditions.
  • Doctors carefully screen donors to make sure the stool is safe.
  • Fecal transplants are usually safe, with mild and temporary side effects like nausea.

How long does it take to recover from a fecal transplant?
You may start feeling an improvement in your symptoms within a day of having a fecal transplant, with full improvement after a week or two.

Are fecal transplants still used today?
Yes. They're a treatment option for repeated C. diff infections.

Who is a good candidate for a fecal transplant?
You may be a good fit for fecal transplant if you have repeated C. diff infections, which can cause diarrhea as well as bleeding, swelling, and pain in your colon. 

What's the success rate of a fecal transplant? 
That depends on which method you use. In general, though, it has an 80% to 95% success rate in stopping C. diff from returning.