Velocity-encoded cine magnetic resonance (MR) imaging provides two-dimensional velocity maps of a cross-sectional area of a vessel. Pulmonary flow and flow patterns in the main pulmonary artery were analyzed with velocity-encoded cine MR imaging and Doppler echocardiography in 10 patients with pulmonary hypertension (PH), one patient with a dilated main pulmonary artery, and 10 healthy subjects, and these findings were compared. Peak systolic velocity measured with velocity-encoded cine MR imaging was similar to that measured with Doppler echocardiography in healthy subjects and in patients with PH. Velocity-encoded cine MR imaging demonstrated substantial differences in velocity across the vascular lumen in PH. The flow pattern in healthy subjects was different than that in patients with PH; the latter had lower peak systolic velocity and greater retrograde flow after middle to late systole. The retrograde flow observed in patients with PH reflected hemodynamic events, since it was inversely proportional to pulmonary flow volume and directly proportional to pulmonary resistance and cross-sectional area of the vessel. Velocity-encoded cine MR imaging demonstrates an inhomogeneous flow profile in PH and may serve as a noninvasive method to estimate pulmonary vascular resistance.