The aims of this study were first to analyze pulmonary flow differences between patients with primary pulmonary hypertension (PPH) and volunteers, and second to determine whether magnetic resonance (MR) 3D Fourier encoding velocity imaging is capable of assessing hemodynamics in PPH. Pulmonary and aortic flows were quantified with MR imaging in 13 patients with PPH confirmed by right heart catheterization (RHC) within the same week and in 10 volunteers. MR pulmonary antegrade velocities, acceleration time (defined as the time from the onset of flow to the peak velocity), and arterial distensibility (maximal surface-minimal surface/minimal surface) were significantly different in patients (p < 0.05). MR pulmonary and aortic flow volumes correlated well with each other in the two populations (r = 0.98). Agreement between MR and RHC data was low: for the right cardiac output (mean difference) the 95% confidence interval was -0.88 to -0.22 L/min and for the right stroke volume 2.83 to 9.71 ml. However, the high coefficient correlations found between the two techniques showed that MR data could be used as indicators of right hemodynamics. 3D Fourier encoding-velocity sequence is a reliable noninvasive flow measurement method for the quantification of right hemodynamics in patients with PPH.