A fecal transplant is a procedure that transfers stool from a donor to the gastrointestinal (GI) tract of another person for the purpose of treating a disease or condition. It’s also called a fecal microbiota transplant (FMT) or bacteriotherapy.

They’re becoming increasingly popular as people become more familiar with the importance of the gut microbiome. The idea behind fecal transplants is that they help to introduce more beneficial bacteria into your GI tract.

In turn, these helpful bacteria may help against a range of health conditions, from GI infections to autism spectrum disorder (ASD).

There are several methods for performing a fecal transplant, each with their own benefits.


This method delivers a liquid stool preparation directly into your large intestine via a colonoscopy. Often, the colonoscopy tube is pushed through the entirety of your large intestine. As the tube withdraws, it deposits the transplant into your intestine.

Use of colonoscopy has the advantage of allowing doctors to visualize areas of your large intestine that may be damaged due to an underlying condition.


Like the colonoscopy approach, this method introduces the transplant directly into your large intestine through an enema.

You may be asked to lie on your side while your lower body is elevated. This makes it easier for the transplant to reach your intestine. Next, a lubricated enema tip is inserted gently into your rectum. The transplant, which is in an enema bag, is then allowed to flow into the rectum.

Fecal transplants given by enema are typically less invasive and lower in cost than colonoscopies.

Nasogastric tube

In this procedure, a liquid stool preparation is delivered to your stomach via a tube that runs through your nose. From your stomach, the tool then travels to your intestines.

First, you’ll be given a drug to stop your stomach from producing acid that could kill helpful organisms in the transplant preparation.

Next, the tube is placed into your nose. Before the procedure, a healthcare professional will check the placement of the tube using imaging technology. Once it’s positioned correctly, they’ll use a syringe to flush the preparation through the tube and into your stomach.


This is a newer method of fecal transplant that involves swallowing a number of pills containing a stool preparation. Compared to other methods, it’s the least invasive and can typically be done in a medical office or even at home.

A 2017 study compared this approach to a colonoscopy in adults with recurring Clostridium difficile infection. The capsule didn’t appear to be any less effective than a colonoscopy in terms of preventing recurring infections for at least 12 weeks.

Still, this method of swallowing capsules requires further study to fully understand its effectiveness and safety.

Following a fecal transplant, you may experience a few side effects, including:

  • abdominal discomfort or cramping
  • constipation
  • bloating
  • diarrhea
  • belching or flatulence

Contact your healthcare provider right away if the pain becomes severe or you also experience:

  • severe abdominal swelling
  • vomiting
  • blood in your stool

The stool used in fecal transplants comes from healthy human donors. Depending on the procedure, the stool is either made into a liquid solution or dried into a grainy substance.

Potential donors must undergo various tests, including:

  • blood tests to check for hepatitis, HIV, and other conditions
  • stool tests and cultures to check for parasites and other signs of an underlying condition

Donors also go through a screening process to determine if they:

  • have taken antibiotics in the past six months
  • have a compromised immune system
  • have a history of high-risk sexual behavior, including intercourse without barrier protection
  • received a tattoo or body piercing in the last six months
  • have a history of drug use
  • have recently traveled to countries with high rates of parasitic infections
  • have a chronic GI condition, such as inflammatory bowel disease

You might come across websites offering fecal samples by mail. If you’re considering a fecal transplant, make sure to work with your healthcare provider to ensure you’re getting a sample from a qualified donor.

C. diffinfections are known for being difficult to treat. About 20 percent of people treated with antibiotics for a C. diff infection will go on to develop a recurring infection. Plus, antibiotic resistance in C. diff has been increasing.

C. diff infections happen when there’s an overgrowth of the bacteria in your GI tract. According to the American College of Gastroenterology, 5 to 15 percent of healthy adults — and 84.4 percent of newborns and healthy infants — have a normal amount of C. diff in their intestines. It doesn’t cause problems and helps in maintaining the normal bacterial population of the gut.

However, other bacteria in your intestines usually keep the population of C. diff in check, preventing it from causing an infection. A fecal transplant can help to reintroduce these bacteria into your GI tract, allowing them to prevent future overgrowth of C. diff.

Evidence check

Most of the existing studies about the use of fecal transplants for the treatment of C. diff infections are small. However, most have produced similar results that indicate a cure rate of more than 90 percent.

Experts have recently been researching how fecal transplants can help with other conditions and health issues, including other GI conditions. Below is a snapshot of some of the research so far.

While some of these results are promising, there’s still a big need for more research in this area to determine the effectiveness and safety of fecal transplants for these uses.

Irritable bowel syndrome (IBS)

One recent review of nine studies found that fecal transplants improved IBS symptoms in 58 percent of participants. However, the nine studies were very diverse in their criteria, structure, and analysis.

Ulcerative colitis (UC)

Four trials were reviewed comparing UC remission rates in people that had received a fecal transplant versus a placebo. Those who received a fecal transplant had a remission rate of 25 percent, compared to 5 percent for those in the placebo group.

Keep in mind that remission refers to a period of time without symptoms. People with UC who are in remission can still go on to have future flare-ups or symptoms.

Autism spectrum disorder (ASD)

A small 2017 trial found that an extended fecal transplant regimen lasting for seven to eight weeks lowered digestive symptoms in children with ASD. Behavioral symptoms of ASD appeared to improve as well.

These improvements were still seen eight weeks after treatment.

Weight loss

A recent study in mice involved two groups: one fed a high-fat diet and another fed a normal-fat diet and placed on an exercise regimen.

The mice on the high-fat diet received fecal transplants from the mice in the second group. This appeared to reduce inflammation and improve metabolism. They even identified several microbes associated with these effects, though it’s unclear how these results will translate in humans.

Read more about the link between weight and gut bacteria.

Who shouldn’t have a fecal transplant?

Fecal transplants aren’t recommended for people who are immunocompromised because of:

While research around fecal transplants is promising, the Food and Drug Administration (FDA) hasn’t approved them for any clinical use and considers them an investigational drug.

Initially, doctors wanting to use fecal transplants had to apply to the FDA before doing the procedure. This involved a lengthy approval process that discouraged many from using fecal transplants.

The FDA has relaxed this requirement for fecal transplants intended to treat recurring C. diff infections that haven’t responded to antibiotics. But doctors still need to apply for any uses outside of this scenario.

The internet is full of information about how to do a fecal transplant at home. And while the DIY route might sound like a good way to get around FDA regulations, it’s generally not a good idea.

Here are a few reasons why:

  • Without proper donor screening, you may be putting yourself at risk of contracting a disease.
  • Doctors who perform fecal transplants have extensive training in how to safely make a stool preparation for transplant.
  • The research into the long-term effects and safety of fecal transplants is still limited, particularly for conditions other than C. diff infection.

Fecal transplants are a promising potential treatment for a range of conditions. Today, they’re used primary to treat recurring C. diff infections.

As experts learn more about the fecal transplants, they may become an option for other conditions, ranging from GI issues to certain developmental conditions.