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Does Medicare Cover an FMT?

Fecal microbiota transplant from healthy in unhealthy intestine, FMT. Improvement intestinal microflora and normalization stool by introducing beneficial bacteria in bowel colon tract. Vector stock illustration
By Daniel Petkevich
Dec 2, 2022

Usually not, but you might qualify

If you are interested in a Fecal Microbiota Transplantation, your coverage might depend on where you live. There currently is no national coverage position, but you might still get coverage if it's deemed medically necessary and you get approval. Let's learn more about if an FMT is right for you.

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What is an FMT and what are its benefits?

Fecal Microbiota Transplantation (FMT) is a medical procedure in which healthy bacteria from one individual's gastrointestinal tract are transplanted into another person's. FMT helps to restore balance in the digestive system, reduce inflammation, and improve overall health. It is particularly beneficial for those suffering from Clostridium difficile (C. difficile) infections, irritable bowel syndrome (IBS), ulcerative colitis, and Crohn's disease, as it has been found to be effective in treating these conditions.

What is the process of getting an FMT?

In most cases, an FMT is offered through a physician or clinic in the form of either a colonoscopy or an enema. After determining that you are a suitable candidate for an FMT, your doctor will collect and prepare the healthy donor stool sample needed for the transplantation. This sample is then carefully injected into your gastrointestinal tract with an endoscope or through an enema.

Medicare coverage of an FMT

At this time, Medicare does not have a national coverage determination for FMT. This means that Medicare will only cover FMT when it's considered medically necessary. If you are interested in this procedure, you should talk with your doctor to determine if it is a viable option for you. In some cases, your doctor may be able to provide the FMT service and bill Medicare for it or refer you to a specialist who does. You should also contact your local Medicare office to see if they have any coverage policies that include FMT.

How much will it cost you to get an FMT done?

The cost of an FMT varies depending on the clinic or doctor performing the procedure and how extensive it is. Generally, you should expect to pay between $2,000 and $5,000 for a full course of treatment. It's important to note that Medicare does not usually cover these costs. Talk with your Medicare plan provider to see what it might cost for your specific situation.

Risks associated with getting FMT done

While an FMT is generally considered safe, there are still some potential risks associated with the procedure. These include allergic reactions to donor stool, infection, and even rare cases of intestinal blockages. It's important to talk to your doctor about these risks before undergoing FMT so that you can make an informed decision about whether or not it is the right choice for you.

How long will the results of the procedure last?

The effects of an FMT typically last for several months but can sometimes be longer, depending on the individual. Continue to follow up with your doctor after undergoing the procedure to monitor your progress and make sure that any conditions you may have are being appropriately managed.

Will I need to take any special precautions after getting the treatment done?

The best way to ensure that you get the most benefit from your FMT is to follow your doctor's instructions for post-treatment care. This may include taking probiotics and/or other medications to help maintain the balance of bacteria in your digestive system and get regular checkups with your physician. Additionally, it's important to continue to practice good hygiene, such as washing your hands frequently and avoiding raw foods that may contain bacteria or parasites. With careful management and proactive care, it's possible to enjoy the long-term benefits of FMT.


Overall, an FMT can be an effective treatment for a variety of conditions and may help improve your overall health and quality of life. Talk to your doctor about whether or not it is a viable option for you, and make sure to inquire about any coverage policies that might apply to you through Medicare. This content is for informational purposes only. Fair Square Medicare is here for you through each step of your Medicare journey. Give us a call today.

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