In patients with Crohn's disease and ulcerative colitis, poor correlation between symptoms and active luminal inflammation has been well established. As a result, the field has moved towards the use of endoscopic assessment to evaluate inflammatory activity. Numerous endoscopic indices have been used for this purpose although none are completely validated. The Simple Endoscopic Score for Crohn's Disease and the Crohn's Disease Endoscopic Index of Severity have been used most frequently; however in addition to incomplete validation, they have important limitations for clinical use, including complexity of scoring and poor reliability of items such as stenosis. The Rutgeerts' score for post-operative Crohn's disease was developed primarily as a prognostic rather than evaluative tool and also requires additional validation. In ulcerative colitis, the Mayo endoscopic subscore has been used as the regulatory standard, although the Ulcerative Colitis Endoscopic Index of Severity may provide a more granular assessment of individual components of disease activity. The use of combined outcomes with patient reported outcomes (PROs) and endoscopic indices has received favor by regulatory bodies but require further validation. This review describes the indications for endoscopic assessment in trials, the indices most frequently utilized for these purposes, and potential future approaches to assessment of disease activity.