The diagnosis of coeliac disease is easy in cases with symptoms and unequivocal small intestinal villous atrophy. However, patients often suffer from only subtle if any symptoms. Borderline villous shortening is common, making the histologic diagnosis difficult. The increase in intraepithelial lymphocytes is typical even in early-stage untreated coeliac disease. Unfortunately, this finding is unspecific. In coeliac disease, the relative density of gammadelta+ intraepithelial lymphocytes is increased. The presence of IgA class anti-endomysium or anti-tissue transglutaminase antibodies clearly increases the likelihood of the disease. Coeliac disease is closely linked to HLA DQ2 and DQ8, and their absence speaks strongly against the condition, whereas a positive finding is virtually of no diagnostic value. In borderline cases, the gluten-dependency of symptoms or mucosal inflammation should be shown by gluten-free diet or gluten challenge. No single test is efficient enough to distinguish unspecific increase in intraepithelial lymphocytes from early coeliac disease; clinical history, histology, serology and gluten-dependency should be taken into account in the diagnostic work-up.