Labeling cells for non-invasive tracking using magnetic resonance imaging (MRI) is an emerging hot topic garnering ever increasing attention, yet it is fraught with numerous methodological challenges, which merit careful attention. Several of the current procedures used to label cells for tracking by MRI take advantage of the intrinsic phagocytic nature of cells to engulf nanoparticles, though cells with low intrinsic phagocytic capacity are also commonly studied. Before we take the next steps towards administering such cells , it is essential to understand how the nanolabel is recognized, internalized, trafficked and distributed within the specific host cell. This is even more critical when contemplating labeling of cells that may ultimately be applied to patients in a therapeutic context.