Esophageal Atresia (EA) with Tracheoesophageal fistula (TEF) can be complicated by aspiration, respiratory distress and other congenital anomalies. We present a case of 1 day old neonate posted for Tracheoesophageal fistula repair who was found to have subglottic stenosis after induction of anaesthesia. A Cormac –Lehane grade 1 direct laryngoscopic view was obtained following induction of anaesthesia, however it was not possible to intubate the patient with  even smallest size 2.0 mm endotracheal tube. Ventilation with size 1 Laryngeal mask airway was adequate. Failed intubation with smallest size endotracheal tube led us to suspect subglottic stenosis. In view of necessity of endotracheal intubation in EA with TEF surgery, this case highlights the importance of management of unexpected subglottic stenosis in neonate in an emergency setting.