A huge thrombosis in the main stem of the pulmonary artery (PA) with pulmonary hypertension has rarely been reported. We present two cases diagnosed and treated in our hospital. One suffered from polyarteritis with a huge thrombus in PA revealed at autopsy. The second case had congenital heart disease of the patent artery duct; and the huge thrombus was found on echocardiogram and extirpated in surgery.