The most frequent cause of villous atrophy is celiac disease (CeD). Typical findings at endoscopy include atrophic villi, fissuring, mosaic pattern. Although these lesions can be well visualized by small bowel capsule endoscopy (SBCE), primary diagnosis is made with serology, upper GI endoscopy, and histology. However, in patients with autoantibody negative villous atrophy, unresponsive course to gluten-free diet (GFD), new symptoms or alarm symptoms as anemia despite GFD, further examination including SBCE is warranted in search of differential diagnoses and complications. Premalignant or malignant complications of celiac disease include refractory celiac disease (RCD), ulcerative jejunitis, enteropathy-associated intestinal T-cell lymphoma (EATL), and small bowel adenocarcinoma. SBCE followed by device-assisted enteroscopy (DAE) where necessary offers a good method for detecting and managing these complications. Differential diagnosis of villous atrophy in particular includes refractory CeD and T-cell lymphoma, autoimmune enteropathy, drug-induced enteropathy, collagenous sprue, tropical sprue, and others.