Autoimmune enteropathy (AE) is an immune mediated illness of the intestinal mucosa. The cause is unknown, and the diagnosis is based on typical characteristics displayed. There is no gold standard for treatment. We present two adult cases of AE and demonstrate the challenges in establishing the diagnosis. The extensive diagnostic work up excluded other more common causes of protracted diarrhoea. Wireless capsule endoscopy (WCE) displayed universal small intestinal mucosal damage with shortened villi that led to the suspicion of AE in both patients. The diagnosis was confirmed with microscopy, showing shortened villi, villous blunting and hyperplasia of crypts in both patients. In one patient, deep crypt lymphocytosis with minimal intraepithelial lymphocytosis was found as well. Both patients were successfully treated with high-dose immunosuppressant therapy to induce and maintain remission. Use of WCE as a diagnostic tool was invaluable in establishing the diagnosis of AE.