Around 50% of patients with ulcerative colitis who undergo ileal pouch–anal anastomosis develop at least one episode of pouchitis. In this Review, Bo Shen describes the aetiology and pathogenesis of pouchitis, particularly the role of dysbiosis andClostridium difficileinfection. Risk factors, clinical features, disease courses and prognoses of pouchitis are discussed, as well as the diagnosis and management of patients with 'conventional' pouchitis and systemic immune-mediated disorders associated with pouchitis.