Autoimmune polyendocrinopathy syndrome type 1 (APS-1) is characterized by the presence of at least two out of three clinical features, which include chronic mucocutaneous candidiasis (CMC), Addison's disease and hypoparathyroidism. The authors' present an one and a half year old girl with recurrent oral thrush who presented with generalised afebrile seizure. Evaluation revealed severe hypocalcemia with low parathormone and normal vitamin D level consistent with hypoparathyroidism. In view of the oral candidiasis and hypoparathyroidism, a clinical possibility of autoimmune polyglandular syndrome (type 1) was strongly considered. Her mother, on subsequent pregnancy was subjected to gene analysis of the fetus (chorionic villus sampling) and also for this child (index case). Both the fetus and index child were confirmed to have the AIRE gene mutation of APS1. After detailed counseling the parents opted for medical termination of the pregnancy. In children who present with recurrent oral thrush we need to consider but also look beyond immunodeficiency.