Villous atrophy may have various etiologies. The diagnosis of villous atrophy relies on an intestinal biopsy which necessitates a perfect histological technique to assert the villous atrophy and its degree. The most frequent etiology is coeliac disease. Villous atrophy regresses with gluten free diet. The failure of a strict gluten free diet implies to exclude a refractory sprue thought to be the earliest form of enteropathy associated T cell lymphoma. The other etiologies of villous atrophy are unusual and could be observed in alpha chain disease, inflammatory and infectious diseases, immune disorders, and primitive ileal villous atrophy. Other etiologies characterize villous atrophy in children as cow milk allergy and epithelial abnormalities.