A system and method for arterial and venous discrimination in MR venography is disclosed. By setting a noise level in the phase image (that is proportional to the velocity encoding value) at a threshold level between that of the arterial signals and the venous signals during the diastole portion of the cardiac cycle and acquiring a phase contrast MR image during the diastole portion, the arterial signals are effectively suppressed and a venous only image can be reconstructed. Post-processing steps are disclosed which can alternatively provide an arterial only image. By separately reconstructing a magnitude image and a phase image map to produce a magnitude image and a phase image, a masking module can create an output displaying venous only or arterial only images based on a user selection. The present invention allows for a complete noninvasive angiography exam to be completed within approximately 30 minutes.