We reviewed the current 'state of the art' on autoimmune enteropathy and small-bowel mucosal atrophy, with the aim of supporting clinicians in a frequently challenging diagnosis through different therapeutic options and prognosis. The diagnosis of small-bowel diseases has radically changed over the last 10 years. The possibility to 'easily' obtain bioptic samples from the jejunum and ileum by means of the enteroscopic techniques (particularly, device-assisted enteroscopy) and the novel cross-sectional imaging studies have opened the window to new insights on intestinal disorders. Consequentially, the detection of small-bowel mucosal atrophy has become a frequent finding in patients undergoing endoscopic investigation and its differential diagnosis can be challenging at times. Among the 'typical' causes of mucosal atrophy, autoimmune enteropathy has become more frequent than previously thought. However, the final diagnosis of autoimmune enteropathy is a 'puzzle' composed by serological, endoscopic, histological and molecular markers, which should be correctly dealt with in order to reach a certain diagnosis. In conclusion, there is an emerging body of literature about autoimmune enteropathy and small-bowel atrophy. The herein presented practical review on autoimmune enteropathy can be of help to clinicians in their daily practice.