Familial adenomatous polyposis (FAP) is an autosomal dominant condition that results in development of the large number of colorectal, and eventually, small intestinal or even gastric adenomas at an early age (late childhood to early adulthood). Extragonadal yolk sac tumors (YSTs) of the gastrointestinal tract are extremely rare neoplasms. Their greater rarity compared with other extragonadal YSTs suggests that different pathogenetic mechanisms could be involved according to the site of origin. Recent epigenetic studies suggest the involvement of some tumor suppressor genes, including the adenomatous polyposis coli gene in testicular YST. No case has so far been described in setting of FAP. Hereby, we describe a case of extragonadal germ cell tumor arising in colectomy stump of a patient with FAP.