In 3-D contrast-enhanced magnetic resonance (MR) angiography of the lower extremities the goal is most often to enhance arterial structures while keeping veins and surrounding tissue unenhanced. Imaging during steady-state concentration of a blood pool agent or during poor timing of an extra-cellular contrast medium may result in simultaneous venous enhancement, making interpretation of the angiogram difficult. The aim of this study was to develop a post-processing method to separate the arteries from the veins in standard contrast-enhanced MR angiograms. The method was based on the different accumulation of flow-induced phase in the arteries and veins of the lower extremities. The method was tested in both phantom experiments and volunteers undergoing 3-D contrast-enhanced MR angiography using both an extra-cellular contrast medium and a blood pool agent. In the phantom studies, opposite directional flow was successfully separated at mean flow velocities as low as 9 cm/s. In the volunteer studies, the larger veins were successfully extinguished while the larger arteries were left unaffected. In smaller vessels with low flow velocities the separation was less successful. This was most apparent in vessels not oriented superior-inferior. The method developed here is promising for separating arteries from veins in contrast-enhanced MR angiography although the results could be further improved by either a different pulse sequence design or combining this method with other segmentation methods.