The causes of pouch dysfunction are inflammatory, non-inflammatory and iatrogenic. The most common long-term complication is pouchitis. Diagnosis should be based on clinical symptoms, endoscopic appearance and histologic findings. Ciprofloxacin and metronidazole are the treatment of choice for pouchitis. Fistulae and perianal abscesses should be suspected to be an expression of misdiagnosed Crohn's disease. Strictures are confronted by endoscopic balloon dilatation. Patients who will be refractory to all forms of medical treatment should have surgical treatment such as faecal diversion or pouch revision.