Intimal sarcoma of the pulmonary artery is an extremely rare type of malignant tumor of the large vessels. Despite systematic diagnostics, distinguishing between pulmonary emboli and tumors is difficult. We report a patient who was referred because of suspected embolic occlusion of the pulmonary artery. The operation was started with the intention of performing a pulmonary artery thromboendarterectomy; however, intraoperative histology revealed a malignant mesenchymal tumor. Therefore, the left lung was resected with the use of extracorporeal circulation, and the pulmonary trunk and right pulmonary artery were reconstructed. A solitary right lung metastasis was resected 3 months later using stapling devices. Complete surgical resection is the treatment of choice for patients with sarcoma of the pulmonary arteries. Surgical therapy often includes extensive reconstructive measures. Since, thromboembolic obstruction cannot be excluded preoperatively, patients with this type of disease should be treated at centers experienced with the broad spectrum of pulmonary artery surgery.