BlueCross and BlueShield of Montana Medical Policy/Codes
Fecal Microbiota Transplantation (FMT)
Chapter: Surgery: Procedures
Current Effective Date: August 27, 2013
Original Effective Date: August 27, 2013
Publish Date: May 27, 2013

Fecal microbiota transplantation (FMT) is an emerging proposed alternative treatment for several gastrointestinal disorders. Previous terms to describe this procedure include fecal bacteriotherapy, fecal microbiota therapy, fecal transfusion, fecal or stool transplant, fecal enema, intestinal microbiota transplant (IMT) and human probiotic infusion (HPI).

FMT has shown some effectiveness in the treatment of intestinal dysbiosis (microbial imbalances), such as inflammatory bowel disease (IBD), ulcerative colitis (UC), constipation, diarrhea, and Clostridium difficile infection (CDI). FMT is being investigated in animal studies as a method to treat obesity, by treating the patient with fecal microbiota from lean donors, as well as neurological disorders (such as anxiety or depression); or autoimmune disorders.

Studies reveal the most common utilization of FMT is the treatment of CDI, which is a frequent cause of diarrhea due to pseudomembranous colitis from taking antibiotics. Infections may become severe, refractory to treatment methods and, in some cases, likely to relapse. The antibiotics may alter the normal gastrointestinal flora, which protect the intestinal pathogenic bacteria. 

FMT involves the restoration of the colonic flora by introducing healthy bacterial flora from a donor via a nasogastric/nasoduodenal tube, enema, or colonoscopy. The procedure may be done as a single or multiple infusions. Donors are generally a healthy close relative or partner to the patient, as they will have the exposure to some of the same bacteria, living in the same environment, and their stools will be a suitable match. Donors are tested for a wide variety of parasitic and bacterial infections, including hepatitis, human immunodeficiency virus (HIV), and syphilis. Genetic differences apparently do not play a role in the reported success of the treatment(s). Once treatment has been performed, the patient may require repeated stool testing to confirm eradication of CDI. Some patients are performing this procedure in the home setting without the direction of a medical provider. It has been reported an additional route of administration is enteric-coated capsules containing saline-filtrated freeze-dried solid stool from the donor.

FMT is not new, as the first use was reported in 1958, with a transplant done via enema in the U.S. The first FMT done by colonoscopy was reported in 2000.

A modified form of FMT had been investigated, known as the autologous restoration of gastrointestinal flora (ARGF) in 2009, which is a self-donation (autologous) of stool provided by the patient prior to medical treatment and stored by refrigeration. If the medical treatment creates intestinal dysbiosis, such as CDI, the stool sample is extracted with saline and filtered, and processed into an enteric-coated capsule, as described earlier. The theory is the replacement of the patient’s original normal gastrointestinal flora, creating a microbial balance.



Blue Cross and Blue Shield of Montana (BCBSMT) considers fecal microbiota transplantation (FMT) experimental, investigational and unproven, including but not limited to the treatment of:

  • Intestinal dysbiosis (such as, inflammatory bowel disease [IBD], ulcerative colitis [UC], constipation, diarrhea, and Clostridium difficile infection [CDI]);
  • Neurological disorders (such as, anxiety or depression);
  • Autoimmune disorders; or
  • Obesity.

Federal Mandate

Federal mandate prohibits denial of any drug, device or biological product fully approved by the FDA as investigational for the Federal Employee Program (FEP). In these instances coverage of these FDA-approved technologies are reviewed on the basis of medical necessity alone.

Policy Guidelines

Codes listed below may be used for both the donor screening and recipient prior or post service.

CPT code 44799 might be reported for the actual instillation of the fecal specimen by nasogastric tube, colonoscopy, or enema.

Rationale for Benefit Administration
This medical policy was developed through consideration of peer reviewed medical literature, FDA approval status, accepted standards of medical practice in Montana, Technology Evaluation Center evaluations, and the concept of medical necessity. BCBSMT reserves the right to make exceptions to policy that benefit the member when advances in technology or new medical information become available.

The purpose of medical policy is to guide coverage decisions and is not intended to influence treatment decisions. Providers are expected to make treatment decisions based on their medical judgment. Blue Cross and Blue Shield of Montana recognizes the rapidly changing nature of technological development and welcomes provider feedback on all medical policies.

When using this policy to determine whether a service, supply, drug or device will be covered, please note that member contract language will take precedence over medical policy when there is a conflict.


Case study series and anecdotal reports suggest the successful outcomes of fecal microbiota transplantation (FMT) in treating a variety of conditions. (1) However, it is infrequently used in part due to an assumption that patients are unwilling to consider FMT as an unpleasant option. Zipursky et al. (2) surveyed 400 individuals, of which 48% (192) responded. Of the 192, 168 (85%) respondents chose to receive FMT, and 29 (15%) chose antibiotics. When the respondents became aware of the fecal nature of the treatment, 16 of the 192 changed their choice from FMT to antibiotics. When asked about the course of administration, more respondents (90%) selected FMT if offered as a capsule. Although most surveyed rated FMT at least “somewhat unappealing”, the respondents indicated they would prefer to receive FMT in the hospital or in the physician’s office.

A MedLine search on the terms fecal transplant, fecal microbiota therapy, and fecal transplantation protocol located 10 articles, one of which was a review of pooled analysis. Reported by Postigo et al. in 2012 (3), a total of 182 patients from 12 published studies were identified. FMT was infused by colonoscopy in 148 patients and 34 by nasogastric tube (NGT). The median age for the colonoscopy group was 72 years, with the NGT group at 82 years. There were differences in the pre-FMT treatment for CDI; 90.5% (134 of 148 patients) of the colonoscopy group received lavage with or without antibiotic and 100% (34 of 34 patients) of the NGT group received lavage without antibiotic. Resolution of the CDI symptoms was determined as clinical success reported by both groups; 93.2% (138/148) in the colonoscopy group compared to the 85.3% (29/34) in the NGT group. The review did not indicate the type of studies reviewed, so it is unknown if they included randomized clinical trials (RCT).

Twenty-six patients with relapsing CDI underwent FMT, via colonoscopy, over a 28-month study period. The authors reported the mean duration of CDI prior to FMT was 12.6 months. Post FMT, the mean duration of follow-up was 10.7 months, in which 24 patients have remained free of significant diarrhea or CDI. (4)

In 2011, a published systematic review of fecal microbacteria therapy by Gough et al. (5) reported 27 case series and reports of 317 patients diagnosed with CDI. The authors reported FMT was highly effective, showing disease resolution in 92% of the case. However, they recommend better designed studies to confirm best practices. This is similar to the 2012 conclusion by Damman et al., in which further clinical studies are required. (1) Their review was to understand the microbiotics role in re-establishing their normal bacteria or shifting their bacteria in the gut back to a healthy state.

Finally an article published in 2012 by Mattila et al. (6) reported on the record review of 70 patients with recurrent CDI that had undergone FMT. Prior to infusion of fecal microbiota cells via colonoscopy, the patients had whole-bowel lavage with polyethylene glycol solution. Clinical failure was defined as persistent or recurrent CDI signs and symptoms. During the first 12 weeks of therapy, symptoms of all patients who did not have the strain of 027 CDI resolved. Of the 36 patients with 027 CDI, 32 had a favorable response and the remaining 4 non responders had a pre-existing serious infection, which was caused by long-lasting diarrheal disease or comorbidity, leading to death as a result of colitis. During the first year after FMT, 4 patients experienced a relapse following antibiotic treatment for an unrelated condition; 2 were treated successfully by additional FMTs and 2 treated with antibiotics.

Regarding the use of FMT to treat obesity, one article was identified providing a theory of utilizing FMT from lean mice donors to germ-free mice. The first human clinical trial in Europe that tested whether FMT helps with metabolic syndrome. They found that 18 obese patients with metabolic syndrome responded better to insulin and had lower triglycerides following FMT from healthy donors. These human subjects did not lose any weight following the FMT. (7)

There have been no published studies located addressing the use of FMT to treat other conditions, including neurological or autoimmune disorders.

The evidence to date is insufficient, including the lack of RCTs or other authoritative guidelines, to permit conclusions on health outcomes concerning the utilization of FMT to treat CDI, other forms of intestinal dysbiosis, or other non-gastrointestinal conditions. Therefore, use of FMT for patients with or without disrupted colonic flora is considered experimental, investigational and unproven.


Disclaimer for coding information on Medical Policies

Procedure and diagnosis codes on Medical Policy documents are included only as a general reference tool for each policy. They may not be all-inclusive.

The presence or absence of procedure, service, supply, device or diagnosis codes in a Medical Policy document has no relevance for determination of benefit coverage for members or reimbursement for providers. Only the written coverage position in a medical policy should be used for such determinations.

Benefit coverage determinations based on written Medical Policy coverage positions must include review of the member’s benefit contract or Summary Plan Description (SPD) for defined coverage vs. non-coverage, benefit exclusions, and benefit limitations such as dollar or duration caps. 

ICD-9 Codes

90.91, 90.92, 90.93, 90.94, 90.95, 90.96, 90.99, 006.9, 007.0, 007.1, 007.2, 007.3, 007.4, 007.5, 007.6, 007.8, 007.9, 009.0, 009.1, 009.2, 009.3, 306.4, 556.0, 556.1, 556.2, 556.3, 556.4, 556.5, 556.8, 556.9, 564.00, 564.09, 569.8, 569.9, 579.0, 579.1, 579.2, 579.8, 579.9, 787.91

ICD-10 Codes

Experimental, Investigational and Unproven for all codes.

Procedural Codes: 44705, 44799, 82270, 82272, 86701, 86702, 86703, 86709, 87045, 87046, 87177, 87230, 87324, 87327, 87328, 87329, 87335, 87336, 87337, 87338, 87340, 87493, 87803, 89125, G0455
  1. Damman, C.J., Miller, S.I., et al. The microbiome and inflammatory bowel disease: is there a therapeutic role for fecal microbiota transplantation? American Journal of Gastroenterology (2012 October) 107(10):1452-9.
  2. Zipursky, J.S., Sidorsky, T.I., et al. Patient attitudes towards the use of fecal microbiota transplantation in the treatment of recurrent Clostridium difficile infection. Clinical Infectious Disease (2012 September 18): Epub ahead of print. Available at (accessed on 2012 October 8).
  3. Postigo, R., and J.H. Kim. Colonoscopic versus nasogastric fecal transplantation for the treatment of Clostridium difficile infection: a review and pooled analysis. Infection (2012 July 31): Epub ahead of print. Available at  (accessed on 2012 October 8).
  4. Kelly, C.R., de Leon, L., et al. Fecal microbiota transplantation for relapsing Clostridium difficile infection in 26 patients: methodology and results. Journal of Clinical Gastroenterology (2012 February) 46(2):145-9.
  5. Gough, E., Shaikah, H., et al. Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection. Clinical Infectious Disease (2011 November) 53(10):994-1002.
  6. Mattila, E., Uusitalo-Seppala, R., et al. Fecal transplantation, through colonoscopy, is effective therapy for recurrent Clostridium difficile infection. Gastroenterology (2012 March) 142(3):490-6.
  7. Luiggi, C. Same poop, different gut. The Scientist (2010 November 3): Epub ahead of print. Available at (accessed on 2012 October 12).
May 2013  New 2013 BCBSMT medical policy.  Fecal microbiota transplantation (FMT) is considered experimental, investigational and unproven.   
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Fecal Microbiota Transplantation (FMT)