MR imaging was able to reveal substantial differences in flow between the systemic arterial and pulmonary venous circulations in patients with chronic thromboembolic pulmonary hypertension. These differences correlated well with the diameters of the bronchial arteries seen on helical CT. Furthermore, these differences resolved after pulmonary thromboendarterectomy. MR imaging enables the accurate estimation of flow in the bronchial arteries in patients with chronic thromboembolic pulmonary hypertension.