Summary Objective  To assess the occurrence of growth hormone deficiency (GHD) in patients with coeliac disease (CD). Study Design  A total of 1066 children diagnosed elsewhere with short stature were referred to our centre for second‐line evaluation in a 6‐year period. All patients were screened for CD by antiendomysial antibodies (EMA) and those with positive sera underwent intestinal biopsy. Results  Among the 1066 short children, 210 (19·7%) had GHD and 12 (1·12%; chronological age from 3·6 to 12·3 years, bone age from 1·5 to 10·5 years, SDS height from −3·05 to −0·48), having positive EMA, showed histologically confirmed CD. Nine of these latter 12 CD children had a beneficial effect on growth rate after the first year of gluten‐free diet, while the remaining three showed no catch‐up growth. A careful endocrinological investigation in these three CD boys showed an isolated GHD in two cases and a multiple GHD in one case. The congenital origin of GHD is supported by the congenital abnormalities documented by magnetic resonance imaging. GH therapy associated with gluten‐free diet led to an increased growth rate. Conclusion  GH secretion should be evaluated in coeliac patients showing no catch‐up growth after a period on a gluten‐free diet in spite of reversion to seronegativity for EMA. In the case of GHD and CD, replacement GH therapy should be started during a gluten‐free diet.