The unexpected diagnosis of Crohn's disease (CD) after restorative proctocolectomy is a relatively frequent occurrence. We report a retrospective analysis of the long-term development of patients with an ileal pouch-anal anastomosis (IPAA) in whom the definitive anatomopathological diagnosis was CD, and compare their development with that of patients in whom the diagnosis of ulcerative colitis (UC) was confirmed. We reviewed the clinical data of 112 patients with an IPAA. The definitive diagnosis was CD in 12, and UC in the rest. The mean follow-up period was 76 months (range 12 to 192). We analyzed and compared the epidemiologic and clinical data, postoperative complications, functional results, anxiety, and quality of life in the two groups. Postoperative morbidity and the degree of satisfaction were similar in the two groups. The test showed a lower level of anxiety and higher quality of life in patients with CD. Of all the functional parameters studied, only urgency of defecation presented a higher risk in the CD group (HR: 4.13, CI: 1.41-12.04, p = 0.027). Despite the fact that a diagnosis of CD is currently considered a contraindication for an IPAA, some patients with secondary diagnosis of CD have good functional outcome and quality of life after restorative proctocolectomy. Closure of the temporary ileostomy may be justified in these patients.