Restorative proctocolectomy with ileal pouch-anal anastomosis (IPAA) is the surgical treatment of choice for ulcerative colitis and familial adenomatous polyposis patients who require surgery. Pouchitis is the most common long-term complication after IPAA. Patients with pouchitis represent a heterogeneous group in terms of pathogenesis, clinical presentation, disease course, and prognosis, suggesting a wide range of disease mechanisms. Before the diagnosis of pouchitis is made, other inflammatory and non-inflammatory disease conditions, such as Crohn's disease, cuffitis, and irritable pouch syndrome, should be ruled out. Pouch endoscopy is the most important tool for diagnosis and differential diagnosis. Accurate diagnosis and classification are essential for appropriate management. Although the majority of patients with pouchitis respond to antibiotic therapy, a subset of these patients cannot achieve remission by means of antibiotics and thus require anti-inflammatory or immunosuppressive treatment.