Familial adenomatous polyposis (FAP) is an autosomal dominant inherited disorder linked to a mutation in the APC gene, associated with the development of multiple colonic and duodenal adenomas, which in 100% of cases progress to colorectal cancer (CRC) if left untreated. Management of affected patients is usually based on prophylactic total colectomy with or without rectal preservation, followed by regular endoscopic surveillance of the duodenum and rectum or ileal reservoir. However, there is considerable inter- and intra-familial variability in the rate of adenoma appearance and development for identical mutations. This strongly suggests the additional role of environmental factors. Recently, the gut microbiota has been identified as a co-factor of carcinogenesis in patients with FAP, but no prospective evaluation of the association between the incidence and severity of adenomatous proliferations and a microbiological signature has been studied, particularly at duodenal level in operated patient.