We describe the applications of new cellular magnetic labeling method to endothelial progenitor cells (EPC), which have therapeutic potential for revascularization. Via their negative surface charges, anionic magnetic nanoparticles adsorb non-specifically to the EPC plasma membrane, thereby triggering efficient spontaneous endocytosis. The label is non-toxic and does not affect the cells’ proliferative capacity. The expression of major membrane proteins involved in neovascularisation is preserved. Labeled cells continue to differentiate in vitro and to form tubular structures in Matrigel (an in vitro model of neovascularization). This process was followed in situ by using high-resolution MRI. Finally, we show that magnetic forces can be used to move magnetically labeled EPC in vitro and to modify their organization in Matrigel both in vitro an in vivo. Magnetic cell targeting opens up new possibilities for vascular tissue engineering and for delivering localized cell-based therapies.