Histological examination of small intestinal biopsies is an essential step in the assessment of malabsorption syndromes. Multiple biopsies should be taken in the proximal jejunum or distal duodenum and correctly oriented. Histological evaluation has to be systematic considering villous architecture, inflammation and specific diagnostic elements. In celiac disease, even with the development of serology tests, the biopsy remains useful to follow the patient and to detect potential complications.