by Jones P
(Fecal transplant)


Fecal microbiota transplantation (FMT) is the transfer of fecal content from a healthy donor into the gut of someone else. The fecal content may be delivered to the gut through:

Reasons for Procedure

There are many germs that live in the gut. Most are helpful but some can cause problems. Some illnesses or treatment can cause an imbalance between good and bad germs. This can lead to infections or symptoms. FMT uses a group of germs from a healthy donor to try to make a healthier germ colony in someone who is ill.

FMT has not been approved for routine treatment. Still, many health centers can use it under the direction of the FDA. FMT may be used to treat some people with an infection called C diff. This infection of the gut often happens after the use of antibiotics. FMT may help C Diff that is severe or keeps coming back.

Research is being done to look at use of FMT for other gut issues.

Possible Complications

All procedures have some risk. Your doctor will review problems that could happen, like:

Some more serious, but rare problems may include:

  • High fever
  • Infection that spreads to other parts of the body
  • Development of autoimmune problems—can happen months or years after FMT

Other problems will depend on how FMT was done. For example, a colonoscopy can cause injury to the gut. Be sure to talk to your care team about what your risks may be.

What to Expect

Prior to Procedure

Other treatments for C Diff are often tried first. Some blood tests may be done to see if FMT is a good choice.

The gut may need to be clear before the procedure. Food and drinks may be limited up to 24 hours before FMT.

Some medicine may also need to be stopped up to 1 week before the procedure.


The type of anesthesia will depend on which method is used. Anesthesia will not be needed if the pill is used.

Description of the Procedure

Tests will be done to make sure the donor is healthy. Stool will be taken from the donor. It will then be made into a liquid mix or pill. The pill will be swallowed. The liquid will be passed inside the gut with:

  • Colonoscopy—A tube is passed through the rectum. It will be moved up into the large bowel. The mix will be passed through the tube into the large bowel.
  • Upper Endoscopy—A tube is passed down throat. It will be moved into the stomach then down into the small intestine. The mix will be passed through the tube into the small intestine.

How Long Will It Take?

Less than 1 hour for procedures

Will It Hurt?

FMT may cause some belly pain.

Procedures may cause some cramping, belly, or throat pain. It is most often mild and passes in 1-2 days.

Post-procedure Care

After the procedure, you may be observed for an hour. Then, you will be able to go home.

Call Your Doctor

It is important to track your recovery. Alert your doctor to any problems. If any of these happen, call your doctor:

  • Signs of infection, such as fever and chills
  • Severe belly pain
  • Hard, swollen belly
  • Trouble swallowing or breathing
  • Any change or increase in your original symptoms
  • Bloody or black tarry colored stools
  • Upset belly and/or throwing up
  • Cough, hard to breathe, or chest pain
  • Bleeding

If you think you have an emergency, call for emergency medical services right away.


American Gastroenterological Association 

American Society for Gastrointestinal Endoscopy 


Canadian Digestive Health Foundation 

Health Canada 


Colonoscopy. National Institute of Diabetes and Digestive and Kidney Diseases website. Available at: Accessed July 2020.

Fecal Microbiota Transplantation. EBSCO DynaMed website. Available at: . Accessed July 2020.

Gupta, S., Allen-Vercoe, E., etc. (2016). Fecal microbiota transplantation: in perspective. Therapeutic advances in gastroenterology, 9(2), 229-239. doi:10.1177/1756283X15607414

Khanna S. Microbiota Replacement: Innovation in Gastrointestinal Care. Clin Pharmacol Ther. 2018 Jan;103(1):102-111. doi: 10.1002/cpt.923. Epub 2017 Nov 14.

Understanding upper endoscopy. American Society for Gastrointestinal Endoscopy website. Available at: Accessed July 2020.

Revision Information

  • Reviewer: EBSCO Medical Review Board Adrienne Carmack, MD
  • Review Date: 07/2020
  • Update Date: 07/19/2020