Optimal management of inflammatory bowel disease (IBD) requires a multidisciplinary team approach, including specialists in the fields of gastroenterology, surgery, radiology and pathology. The histological examination of endoscopic biopsies or resection specimens after surgery aids in establishing the diagnosis of IBD and plays a central part in distinguishing between the two main entities of IBD, that is ulcerative colitis (UC) and Crohn’s disease (CD). The histopathological features that are characteristic for either UC or CD, have been well-described for decades. Though, the fact that no single finding is truly disease specific can introduce diagnostic doubt and mix-up of the diagnoses. Recent progress in the usage of proper validated histological indexes to measure and grade the histological activity in endoscopic biopsies, and the systematical evaluation of resection margins in ileal resections specimens in CD, suggest that histological assessment can be utilized as a predictive factor that can guide disease management, also after the diagnosis has been established. For now, systematic assessment of histological activity with an appropriate histological index is a well-established endpoint for evaluation of treatment responses in clinical trials. Given the growing amount of valid data, it might also be beneficial to systematically include use of histological scoring in daily clinical practice to improve the future management of IBD.