Pulmonary thromboendarterectomy was performed on two patients with chronic pulmonary thromboembolism showing thrombotic tendency. Patient 1 was a 25-year-old male with the disease complicated by congenital antithrombin III deficiency. Patient 2 was a 21-year-old male with the disease complicated by antiphospholipid syndrome. Both patients were admitted to the center upon showing dyspnea. Lung perfusion scintigraphy revealed multiple defects in the right and left lungs. Pulmonary arteriography showed occlusion and stenosis from lobar to segmental arteries. Cardiac catheterization showed marked pulmonary hypertension. Pulmonary angioscopy confirmed the presence of organized thrombi while an intravascular ultrasound revealed a thickening of the pulmonary arterial walls in both lungs. After the insertion of an inferior vena cava filter in each patient, surgery was performed. Following a median sternotomy, a cardiopulmonary bypass was utilized to induce deep hypothermia at a pharyngeal temperature of 16 degrees C, after which a thromboendarterectomy of the bilateral pulmonary arteries was performed under intermittent circulatory arrest. A large amount of organized thrombi was extracted from these arteries. After surgery, both patients showed good postoperative outcome with improved blood flow in both lungs, reduced pulmonary arterial pressure and increased cardiac output.