Treatment of ulcerative colitis (UC) and Crohn’s disease (CD) represents, in the majority of cases, a real challenge to the gastroenterologist’s abilities and skills as well as a clinical test concerning his/her levels of medical knowledge and experience. During the last two decades, our pharmaceutical arsenal was significantly strengthened, especially after the introduction of the so-called biological agents, drugs which to a large extent not only improved the results of conservative treatment but also changed the natural history of the disease. However, colectomy is still necessary for some patients with severe UC although smaller compared to the past, precisely because of the improvements achieved in the available conservative treatment. Nevertheless, surgeries to treat colon dysplasia and cancer are increasing to some extent. At the same time, satisfactory improvements in surgical techniques, the pre-and post-operative care of patients, as well as the selection of the appropriate time for performing the surgery have been noticed. Regarding patients with CD, the improvement of conservative treatment did not significantly change the need for surgical treatment since two-thirds of patients need to undergo surgery at some point in the course of their disease. On the other hand, the outcome of the operation has improved through good preoperative care as well as the wide application of more conservative surgical techniques aimed at keeping as much of the bowel in situ as possible. This article discusses the indications for surgical management of UC patients from the gastroenterologist’s point of view, the results of the emerging new techniques such as transanal surgery and robotics, as well as alternative operations to the classic ileo-anal-pouch anastomosis. The author also discusses the basic principles of surgical management of patients with CD based on the results of the relevant literature. The self-evident is emphasized, that is, to achieve an excellent therapeutic result in patients with severe inflammatory bowel disease in today’s era; the close cooperation of gastroenterologists with surgeons, pathologists, imaging, and nutritionists is of paramount importance.