Biopsy assessment of chronic idiopathic inflammatory bowel disease (IBD) is important for diagnosis, classification, determination of activity, documentation of anatomical extent and distribution, detection of complications, and diagnosis and grading of dysplasia. In addition, it may predict treatment response, clinical behaviour after therapy, and risk of future dysplasia. Microscopic features favouring IBD over non-IBD in biopsies include basal plasmacytosis and crypt architectural changes. Typically, ulcerative colitis (UC) extends from the rectum proximally and in a continuous fashion, while Crohn’s disease is discontinuous with intervening areas of sparing. Microscopic features that distinguish most reliably between Crohn’s disease and UC include granulomas (strongly favouring Crohn’s disease) and the distribution of architectural abnormalities/chronic inflammation between sites and within sites. However, discontinuity may also occur in UC. A caecal ‘patch’, i.e. a discontinuous area of caecal inflammation, is common in UC. Rectal sparing and other forms of discontinuity are more frequent in longstanding UC than new UC. The label IBD unclassified (IBDU) is available for difficult cases. In very early IBD (i.e., symptoms for <6 weeks), the architectural changes are often absent. IBD is common in patients with primary sclerosing cholangitis but may have unusual features. In summary, histological assessment in the light of the clinical and endoscopic findings plays an important role in optimising management of IBD.