Small bowel villous atrophy is most often caused by celiac disease in the Western world, but other diseases should be explored in patients without positive serology. Adult-onset autoimmune enteropathy (AIE) is a rare cause of villous atrophy first known in children with T-cell dysregulation but also seen in adults with autoimmune predispositions. Here, an 82-year-old woman with autoimmune thyroiditis was admitted with weight loss and watery diarrhoea not responding to diet change. Endoscopy revealed villous atrophy both in the duodenum and in the ileum, but no positive celiac serology. A diagnosis of autoimmune enteropathy was made based on chronic diarrhoea not responding to diet change, autoimmune predisposition, villous atrophy, typical histological findings, and no evidence of immunodeficiency or medications causing villous atrophy. The patient was treated to good effect with corticosteroids but needed total parenteral nutrition while admitted. AIE should be considered in villous atrophy without positive celiac serology.