Atypical celiac disease (ACD) presenting in childhood has rarely been documented from India. The present retrospective study analyzed features of atypical celiac disease over a 5-year period. Patients were diagnosed to have Celiac Disease (CD) as per the standard ESPGHAN criteria. The biochemical and hematological parameters of the cohort of children presenting with atypical features (ACD) were compared with children presenting as typical diarrheal CD. Twelve children were diagnosed to have CD. Seven of them presented with ACD. The two groups did not differ significantly in their age of presentation, hematological and biochemical profile. Osteoporosis as documented on bone mineral densitometry was present in all 6 patients of ACD in whom BMD was done. Short stature (4) and refractory iron deficiency anaemia (3) was the commonest modes of presentation of ACD. Occurrence of these conditions either singly or in combination warrants exclusion of celiac disease in children.