Acute pulmonary embolus (less than 6 weeks old) has been considered an absolute contraindication to heart transplantation for fear of the potential problems of lung abscess, empyema, bronchopleural fistula, and systemic sepsis in an immunosuppressed patient. It is difficult to adhere to this principle because 30% to 50% of patients with dilated cardiomyopathy may have an acute pulmonary embolus and would be excluded from transplantation. Several centers have considered such patients for heart transplantation if they are young, on maximal medical therapy, and in extremis. The surgical management of the postoperative pulmonary problems can include bronchoscopy, antibiotics, surgical drainage, decortication, and pulmonary resection with or without muscle flaps. We describe our approach to two such patients who were managed successfully with lobectomies and latissimus dorsi muscle flaps to seal the bronchus and fill the pleural space.