In patients suffering from reflux esophagitis, the severity of the lesions helps to predict the prognosis and adapt treatment. We herein review the data which suggest that endoscopy also has a prognostic value in inflammatory bowel disease. In the 1990s, the general opinion, based on a few studies, was that assessing endoscopic lesions was not critical for the management of inflammatory bowel disease. The more recent therapeutic strategies using less steroids but purine analogs and anti-TNF antibodies have led to a higher chance of mucosal healing (MH), and there is growing evidence that reaching healing of lesions is of good prognostic value both in ulcerative colitis and Crohn's disease. There is a lower risk of hospitalization and of surgery in patients with MH than in those without healing. There is also a (moderately) lower risk of relapse after stopping treatments in patients with MH than in those with persistent lesions. The risk of cancer (on a long-term basis) also seems be lower in patients with controlled inflammatory lesions than in subjects with persistent inflammation. There are still many unanswered questions, the major one being what is the best treatment choice when MH is not reached?