Endothelial progenitor cells (EPCs), originating from bone marrow, play a significant role in the repair of ischemic tissue and injured blood vessels. They are also involved in tumor angiogenesis. The therapeutic potential of EPCs for regenerative medicine and cancer treatment calls for new methods for monitoring and controlling cell migration. This review focuses on promising magnetic methods based on the internalization of magnetic nanoparticles by EPCs. We first describe the cellular uptake of iron oxide nanoparticles depending on their surface properties. We thus review the use of MRI for the detection of labeled cells and for noninvasive follow-up of EPCs homing in sites of endothelium regeneration. Finally, we show that remotely applied magnetic forces may enable intracellular manipulation and may optimize cell-delivery strategies for localizing cell therapy to target sites.