Surgery improves the quality of life in patients with Crohn's disease (CD) and cures patients with chronic ulcerative colitis (CUC). There are several surgical controversies primarily involving techniques and long-term outcomes. Some debates are long standing; whether to perform a double-stapled ileal pouch-anal anastomosis (IPAA) or a mucosectomy and hand-sewn anastomosis, and whether to divert or not to divert in patients with CUC undergoing an IPAA. Other issues are more recent, such as the effects of age, pregnancy, pouch salvage, and laparoscopic IPAA. In patients with Crohn's disease the anastomosis technique, the management of perianal disease, and the role of laparoscopic surgery are topics of debate. This review shows the current concepts and controversies in the surgical management of patients with CUC or CD.