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Coding: Fecal Microbiota Transplant (FMT) Guidance

Follow these guidelines to properly code and bill private payors and Medicare for the FMT procedure.

AGA is committed to providing practical guidance to GIs using fecal microbiota transplant (FMT) to treat patients. Follow these guidelines to properly code and bill private payors and Medicare for the procedure.

Coding and billing FMT donor and recipient procedures for commercial payors.  

Report an appropriate level E/M code for the specimen collection.

Report the appropriate laboratory testing and ICD-9/10 codes for testing the donor for infectious pathogens to rule out unsuitable specimens.

Supporting ICD-10-CM codes for labs performed on donor specimen.

ICD-10 CodeICD-10 Descriptor
V20.9Contact with and (suspected) exposure to unspecified communicable disease
Z22.1Carrier of other intestinal infectious diseases
Z11.59Encounter for screening for other viral diseases
Z11.3Encounter for screening for infections with a predominantly sexual mode of transmission
Z11.2Encounter for screening for other bacterial diseases
Z11.0Encounter for screening for intestinal infectious diseases
Z11.8Encounter for screening for other infectious and parasitic diseases
Z11.9Encounter for screening for infectious and parasitic diseases, unspecified

Do not report 44705 if the specimen is unsuitable for transplantation.

If the specimen is suitable for transplantation then code 44705 can be reported. Unless otherwise specified by the payor, the preparation of the donor specimen is typically covered by the recipient’s insurance.

44705, Preparation of fecal microbiota for instillation, including assessment of donor specimen

The instillation of microbiota is separately reported. For instillation of microbiota by oro-nasogastric tube or enema, use 44799. For instillation via esophagogastroduodenoscopy (EGD) or colonoscopy, use the appropriate CPT code for upper gastrointestinal endoscopy or colonoscopy.

Do not report 44705 in conjunction with 74283 (Therapeutic enema, contrast or air, for reduction of intussusception or other intraluminal obstruction (e.g., meconium ileus)).

NOTE: Code 44705 has a Medicare Physician Fee Schedule procedure status indicator of I (Not valid for Medicare purposes) and should not be used to report FMT for Medicare beneficiaries. See Coding and billing FMT recipient procedures for Medicare beneficiaries below.

Coding and billing FMT recipient procedures for Medicare beneficiaries

G0455, Preparation with instillation of fecal microbiota by any method, including assessment of donor specimen

HCPCS code G0455 includes the work of preparation AND instillation of the microbiota. Medicare does not pay a separate fee for the installation of the microbiota by oro-nasogastric tube, enema, or by upper or lower endoscopy. 

Only the donor specimen that is ultimately used for the treatment of the beneficiary can be billed in conjunction with the instillation. Medicare does not cover the costs of screening of the donor specimen, thus beneficiaries should be advised of the cost of screening, which they may be at risk of paying for out-of-pocket. This may require the physician to provide an Advanced Beneficiary Notice of Non-coverage (ABN) Form to the donor and recipient.