The fatal outcome in an eleven-year-old girl, one month after an extra-cardiac Fontan operation is reported. She was diagnosed with tricuspid atresia and had a Blalock Taussig shunt and a bidirectional Glenn procedure. The Fontan operation was performed using a Dacron conduit, fenestrated with a 6 mm Goretex tube. The first week after the operation she received low molecular weight heparin, then it was stopped and aspirin was started. One month after surgery she was admitted to the hospital because of sudden cyanosis, dyspnea, chest pain and syncope. A diagnosis of left pulmonary artery thrombosis without right to left shunt across the fenestrated tube was made. She was carried to the cardiac catheterization laboratory where a mechanical lysis of the thrombi was attempted. A local infusion of rtPA was started without improvement and she died 3 hours later.