BACKGROUND Several studies have suggested a link between coeliac disease and other autoimmune diseases. AIM To compare the presence of autoimmune disease in children with coeliac disease and in controls. METHODS When coeliac disease was diagnosed, 267 children were evaluated for clinical autoimmune disease (with signs/symptoms), subclinical autoimmune disease (with autoantibodies and subclinical impairment of the target organ) or potential autoimmune disease (with autoantibodies only) and compared with 220 healthy controls. 170 coeliac disease patients were followed up for a mean 47 +/- 31 months, in complete remission on a gluten-free diet. Ninety-nine controls were followed up for 45 +/- 33 months. RESULTS When coeliac disease was diagnosed, 71 (27%) children had autoimmune disease vs. 1% among the controls (P < 0.001): 31 had clinical autoimmune disease and 40 had subclinical or potential autoimmune disease. During the follow-up, the clinical autoimmune disease cases slightly decreased from 12% to 11%, while the potential autoimmune disease cases increased from 14% to 21%. Of the 99 controls, none had any variation in their autoantibody profile. CONCLUSIONS Gluten-free diet does not modify the natural history of autoimmunity in patients with coeliac disease. However, gluten-free diet seems to produce a favourable effect on the previously present clinical autoimmune disease and to prevent the development of new clinical autoimmune disease, but does not affect the onset of potential autoimmunity, which tends to increase with time.