OBJECTIVE To determine the prevalence of celiac disease (CD) in children with idiopathic short stature (ISS) and the diagnostic value of immunoglobulin (Ig) A G antigliadin antibodies (AGA) and transglutaminase (TTG) antibodies for CD. METHODS A total of 104 children (49 male, 55 female) with ISS without a specific etiology were studied. Extensive endocrine investigations had shown no abnormalities in any subject. Anthropometric parameters and IgA AGA and IgA TTG antibodies were evaluated in this study group. These antibodies were measured by enzyme-linked immunosorbent assay. All patients were referred for an endoscopic intestinal biopsy. The biopsy samples were classified according to revised Marsh criteria (UEGW 2001). RESULTS We detected positive IgA TTG antibodies in 36 and IgA AGA in 35 of these patients. Thirty one IgA TTG antibody positive and 28 IgA AGA positive subjects showed histological abnormalities compatible with celiac disease (33.6%). Sensitivity, specificity, positive predictive value (PPV) and negative predictive value for IgA AGA were found to be 80%, 88.4%, 77.8% and 89.7%, respectively. Sensitivity, specificity and PPV for IgA TTG antibodies were 88.6%, 94.2% and 88.6%, respectively. CONCLUSIONS We conclude that the prevalence of celiac disease is high in patients with ISS and it is important to test all children with ISS for celiac disease by measuring serologic markers and performing an intestinal biopsy.