FMT Regulations

In 2013 the Food and Drug Administration (FDA) recognized FMT was being used as treatment for a variety of diseases and therefore created a policy regarding its use. In order to monitor and continue the evolution of its use, it was designated as an Investigational New Drug (IND). Normally, this designation would require an IND application and approval to use FMT with patients. However, concern about the life saving and time sensitive nature of its use with Clostridium difficile (C.diff) infections led to special guidance. This guidance outlines discretionary enforcement in the case of C.diff infections not responding to standard therapies. 

FDA FMT Guidance

FMT Summary

  • In 2013 the FDA released guidance relating to FMT that restricts its use as an IND with an exception for C.diff not responding to standard treatments.

  • The FDA guidance allows physicians to treat patients with FMT who have C.diff not responding to standard therapy as long as they obtain informed consent.

  • The FDA 2016 draft guidance was never enacted so the current regulations do not require donors to be “known” to either the patient or physician.

  • FDA does not specify the delivery route of FMT or a standardized process for preparation of FMT.

  • Treatment for anything other than C. diff not responsive to standard therapy must be done as part of an IND application through the FDA approval process.

  • Autologous FMT is still considered an IND and is regulated as such.


Excerpt from the 2013 FDA Draft Guidance:


We, FDA, are informing members of the medical and scientific community, and other interested persons that we intend to exercise enforcement discretion regarding the investigational new drug (IND) requirements for the use of fecal microbiota for transplantation (FMT) to treat Clostridium difficile (C. difficile) infection not responding to standard therapies. FDA intends to exercise this discretion provided that the treating physician obtains adequate informed consent from the patient or his or her legally authorized representative for the use of FMT products. Informed consent should include, at a minimum, a statement that the use of FMT products to treat C. difficile is investigational and a discussion of its potential risks. 

FDA FMT Guidance

OpenBiome is the non-profit leader in delivering FMT to physicians in the United States. They have created an excellent summary of the current status of FMT regulation. A portion of that summary is shared below. Flora Medicine encourages all physicians and patients to utilize the OpenBiome website to learn about FMT and its use. They have provided tens of thousands of FMT to patients suffering from C.diff infection (CDI) and provide a wide variety of resources on their website for both physicians and patients. 


Can physicians perform FMT without an IND application (outside of a clinical trial)? 

Yes, to treat patients with C. difficile infections not responsive to standard therapy. When the FDA announced in May 2013 that it would regulate fecal microbiota as an investigational drug, medical professional societies, physicians, and patients reacted with concern over how the policy would limit access to a therapy with 90% efficacy rates for this illness and no known short-term safety risks (Kassam et al., 2013). 

Responding to these concerns, FDA issued guidance in July 2013 stating that it would exercise “enforcement discretion” – that is, it would allow doctors to provide FMT (for patients with C. difficile infections not responding to standard therapies) without filing an IND application." 

FDA FMT Guidance

What are the conditions for performing FMT without an IND application?

Physicians may only use FMT without an IND application to treat patients with C. difficile not responsive to standard therapy. Physicians must also obtain adequate informed consent from the patient or a legal representative, that includes, at minimum, a statement that the use of FMT products to treat CDI is investigational, and a discussion of the therapy’s potential risks and alternative options. 

There are no FDA requirements about how to obtain stool for FMT. Physicians may use material from a donor identified by the patient or physician, or from a universal stool bank. There are also no requirements dictating the route of administration for FMT (e.g. colonoscopy, naso-enteric delivery, oral capsule)." 

FDA FMT Guidance

I have seen a draft FDA guidance stating that physicians using stool from a stool bank must do so under IND. Is this the new policy? 

 In March 2016, FDA released its second draft guidance to propose that enforcement discretion be narrowed so that physicians who obtain material from stool banks to treat CDI that is not responsive to stand therapy do so under IND. This document is a draft for discussion purposes, and does not alter current enforcement discretion policy. 

The prevailing FDA guidance, published in July 2013, states that physicians may perform FMT outside of an Investigational New Drug (IND) application to treat CDI that is not responsive to standard therapy, so long as they obtain informed consent." 


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