Tracheal injury is a rare complication of endo-tracheal intubation. However in neonates, the rates of morbidity and mortality are high. Recommendations for treatment are based on the several reports of this injury and are individualized. Conservative management can be effective in some cases. We describe the case of a neonate who presented with subcutaneous emphysema after intubation in a neonatal intensive care unit. This patient suffered full VACTERL syndrome and had 1.7 mm diameter subglottic stenosis. Conservative management resulted in no further increase in subcutaneous emphysema and after 10 days the patient was stable.