Extracorporeal membrane oxygenation (ECMO) is widely used for neonatal respiratory failure that is potentially reversible but unresponsive to conventional management. Because of the anticoagulation necessary for maintaining the extracorporeal circuit, hemorrhagic complications occur in up to one third of patients. We present an unusual and previously unreported complication of ECMO, total tracheobronchial thrombosis. The thrombus filled the entire lower respiratory tract and resulted in airway obstruction and inability to ventilate. The airway was successfully managed with repeated bronchoscopic pulmonary toilet. Our experience and review of the literature provide a summary of ECMO-related complications likely to present to the otolaryngologist, and management strategies are discussed.