This study aimed to assess the value of IgA-antigliadin and antiendomysium antibodies for coeliac disease screening in children with short stature. In 118 children with height less than the 3rd percentile for age preliminary work-up included absorption, hormonal and genetic studies, sweat test, X-ray for bone age, serum immunoglobulin levels and antigliadin antibodies. In 65 patients antiendomysium antibody and a small-intestinal biopsy were performed. Forty-three children had a normal mucosa and 22 a subtotal villous atrophy. Three coeliac children were negative for both antigliadin and antiendomysium antibodies; one further 11-year-old boy was negative only for antiendomysium antibodies. Sensitivity and specificity for antigliadin antibodies were 94.75% and 93%, respectively, and for antiendomysium antibodies 88.3% and 90.5%. Our results show that the use of antiendomysium antibodies as a confirmatory test to select patients for biopsy could result in coeliac disease going undiagnosed in adolescents.