Coeliac disease is a common disease, affecting 1% of the population. Clinical manifestations are multiple. The diagnosis requires serologic testing and a duodenal biopsy that shows the characteristic findings of intraepithelial lymphocytosis, crypt hyperplasia and villous atrophy, and a positive response to a gluten-free diet. In most patients, the histological diagnosis is easily established. Pitfalls in the pathological diagnosis include a poorly orientated biopsy specimen, either an inadequate biopsy sampling in patients with patchy villous atrophy and the other causes of villous atrophy. A non-response to the gluten-free diet needs to reassess first, the initial diagnosis, second to be sure of the gluten-free diet adherence, and third, to exclude malignant complications such as refractory celiac disease or enteropathy-associated T-cell lymphoma.