Familial adenomatous polyposis (FAP) and Crohn's disease (CD) are two entities with no known etiologic or physiopathogenic relation. The rarity of the former makes the coincidence of both diagnoses in one patient very unlikely. Nevertheless, management in such cases can be puzzling as surgical options must be considered, and immunosuppression/immunomodulation is set in a territory of accelerated carcinogenesis. We report the case of a 29-year-old male with a diagnosis of FAP since adolescence, already submitted to prophylactic proctocolectomy, presenting with anemia and bloody diarrhea, revealing small bowel CD. This case allows for a rich discussion of the clinical dilemmas presenting when FAP and CD are diagnosed in the same patient and for a deep analysis of the concerns inherent to the available therapeutic options.