The development of the ileal pouch anal anastomosis (IPAA) has led to significant improvements in the quality of life for patients after proctocolectomy. The complex anatomy of the pouch requires a systematic examination of the different IPAA components at pouchoscopy and sampling of different histological zones, i.e. pre-pouch, pouch, rectal cuff, and anal mucosa. The main roles of the pathologist are to corroborate a clinical diagnosis of pouchitis, to identify secondary causes of inflammation when present, to be aware of the differential diagnosis, and to exclude histologically identifiable complications such as CMV infection, dysplasia and malignancy. Assessment can be difficult for several reasons, e.g. the anatomical location of a biopsy is not always obvious, adaptive changes may occur that lead to alterations in mucosal morphology, and Crohn’s-like changes may occur as a consequence of pouchitis and may cause diagnostic confusion.