It is becoming increasingly recognized that purely clinical endpoints may not be sufficient in the treatment of patients with inflammatory bowel disease. As such, mucosal disease assessment has become a prominent component of the majority of recent clinical trials in Crohn's disease and ulcerative colitis. There is mounting evidence that the attainment of mucosal healing leads to improved clinical outcomes in both Crohn's disease and ulcerative colitis. However, the use of mucosal healing as a therapeutic endpoint in inflammatory bowel disease is in its early stages, as a number of issues limit its application to routine clinical practice.