Background In this retrospective study, 28 years of surgical treatment of children and young adults with familial adenomatous polyposis (FAP) was analyzed. Methods Forty-three patients were operated on before the age of 26 years. Endoscopic aspects, operative data, and complications were analyzed, and the resection specimens were reevaluated. Functional outcome was assessed by telephone questionnaire. Results Primary ileorectal anastomosis (IRA) was performed in 34 patients with a mean age of 16 years (range, 7-25 years). Primary ileal-pouch anal anastomosis (IPAA) was performed in 9 patients at a mean age of 19 years (range, 15-24 years). Secondary excision of the rectum was performed in 7 patients. Overall, rectal carcinoma was present in 4 patients, at the age of 35, 36, 37, and 38 years. Two patients, aged 39 and 40 years, died because of invasive carcinoma with distant metastasis. The functional outcome and postoperative complications after both procedures were similar to those described in literature for children with FAP. Most patients did not experience alterations in lifestyle, and there was no urinary incontinence. Conclusions In this retrospective study, both IRA and IPAA showed to be feasible techniques in young patients with FAP. A prospective study with a sufficient follow-up is needed to compare both techniques in this specific group of patients.