Patients with coeliac disease may have osteomalacia or osteoporosis, even in the absence of abdominal symptoms. Little is known about the effects of a gluten-free diet and villous restitution on the bone mineral density in adult patients with coeliac disease. Of the 288 patients with coeliac disease in our unit, 13 (5%) had persistent villous atrophy of the small bowel despite dietary recommendations over at least the previous 4 years. For each of these 13 patients, 1 or 2 controls with coeliac disease, matched for age, gender, menopausal state, and dermatitis herpetiformis, whose intestinal mucosa had normalized at least 4 years earlier, were identified (n = 17). Bone mineral density was measured in the forearm using single-photon absorptiometry and in the femoral neck and trochanter using dual-energy X-ray absorptiometry. Bone mineral density was reduced at all sites in patients with persistent villous atrophy compared with patients responsive to diet and healthy controls. Bone mineral density in patients responsive to diet did not differ from that in healthy controls. Persistent villous atrophy is associated with low bone mineral density, underlining the importance of keeping to a proper diet.