Endoscopic assessment of mucosal lesions has emerged as an important concept of disease activity in inflammatory bowel disease (IBD), and recently mucosal healing has generally been regarded as a therapeutic goal not only in ulcerative colitis (UC) but also in Crohn’s disease (CD). Several pieces of evidence have now accumulated to show that mucosal healing determined by endoscopy can alter the course of IBD, as it is associated with sustained clinical remission, and reduced rates of hospitalization and surgical resection. Generally, clinical activity indices established in IBD are mainly determined based on subjective/objective signs and the results of laboratory tests. However, those indices sometimes lead to discrepancy compared with endoscopic indices. Although endoscopy has been rarely investigated as a predictor of the clinical course of IBD, there is now growing evidence that morphological examination, including endoscopy, may help to identify among IBD patients those who should be treated with more intensive treatments. Furthermore, as demonstrated in a recent study assessing early intervention with combination of biologics and immunomodulators, endoscopy may help to select patients who will obtain the best results with early intervention. This chapter summarizes the role of endoscopy in IBD by introducing several modalities such as colonoscopy, balloon-assisted enteroscopy, and video capsule endoscopy, as well as CT colonography and MR enterography.