Pouchitis is an idiopathic inflammatory bowel disease, which occurs in up to 50% of patients operated on for ulcerative colitis with ileal pouch-anal anastomosis (IPAA). Treatment of pouchitis is still to a large extent empirical, but recently more randomized, double-blind placebo-controlled trials have been conducted. This article reviews the possible treatments for pouchitis, focusing especially on treatment with probiotics, which seem to be a new and promising alternative to antibiotics. We are currently doing clinical trials to determine whether a probiotic is an effective treatment for chronic inflammatory bowel disease.