Introduction To screen for coeliac disease in Egyptian children with non-endocrinal short stature, refractory iron deficiency anaemia and type 1 diabetes. Also, to evaluate the sensitivity and specificity of different serological tests for diagnosis of coeliac disease (CD). Material and methods The study included 292 patients with clinical risk of CD. Testing for coeliac antibodies was performed, together with upper gastrointestinal endoscopy and small intestinal biopsy. Results Eleven patients (44%) among 25 patients with refractory iron deficiency anaemia, 23 patients (34.3%) among 67 patients with non-endocrinal short stature, and 6 patients (3%) among 200 patients with type I diabetes mellitus were diagnosed by jejunal biopsy as having coeliac disease. AGA (IgG) had the highest sensitivity for diagnosing CD (80.0%) followed by the TTG (72.7%) antibody, while ARA had the highest specificity (95.9%) followed by anti-EMA (94.7%). Conclusions Coeliac disease is more common in Egyptian children with refractory iron deficiency anaemia, non-endocrinal short stature and type 1 diabetes than was previously thought; therefore it is mandatory to screen such patients for CD. Serological tests showed fairly good sensitivity and specificity for the diagnosis; however, intestinal biopsy remains the cornerstone for definitive diagnosis of patients with immunological reaction to gluten.