This report illustrates the rare occurrence of a pulmonary embolus in a neonate during cardiac catheterization. The patient was a term newborn who underwent repair of obstructed infradiaphragmatic total anomalous pulmonary venous connection. Postoperative risk factors for pulmonary embolism included severe pulmonary hypertension unresponsive to nitric oxide therapy, an indwelling venous catheter, and young age. Successful management was achieved by initial mechanical fragmentation with streptokinase infusion and monitoring by serial lung perfusion scans.