The role of histology in inflammatory bowel disease (IBD) has not yet been well defined. Endoscopic mucosal healing has been proposed as a predictor of the clinical course of IBD and it is indeed considered one of the main therapeutic targets. However, it does not necessarily imply histological healing. Histological remission has been reported to be associated with a better clinical outcome than endoscopic remission only in IBD patients. These observations support the view that histology plays a role as a potential therapeutic target in Crohn's disease and ulcerative colitis. Histological scores being able to quantify the degree of microscopic activity are needed for this purpose. In the era of biologics, indication for proper treatment may benefit from the assessment of clinical and endoscopic activity, as well as histological scores. Such scores may allow us to quantify the microscopic mucosal response to treatment and to define complete healing in IBD. A validated histological score in IBD may lead to the definition of microscopic activity in clinical practice, trials and investigational settings. Several attempts to develop such scores have been reported, but few are currently used and none is applied worldwide in clinical practice. The present review summarizes the main histological scores currently used for assessing IBD activity.