October 2025 page 18
Coding Clarification: Reporting Fecal Microbiota Transplant (FMT) Services
This coding clarification provides updated guidance on fecal microbiota transplant (FMT) that supersedes previous instructions found in the Frequently Asked Questions (FAQ) section in the May 2013 issue of CPT® Assistant (CPTA).
For non-Medicare patients, endoscopic services may be separately reported with previous instruction to use the appropriate code for an upper gastrointestinal endoscopy or colonoscopy if the microbiota instillation is performed via esophagogastroduodenoscopy (EGD) or colonoscopy. For microbiota instillation by oro-nasogastric tube or enema, use unlisted code 44799.
Currently, there is no specific code to report...
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