Advances in stem cell research have provided important understanding of the cell biology and offered great promise for developing new strategies for tissue regeneration. Dynamic determination of stem cell migration and distribution in real time is essential for optimizing treatments in preclinical models and designing clinical protocols. Recent developments in the use of nanotechnologies have contributed to advance of the high-resolution in vivo imaging methods, including the positron emission tomography, the single-photon emission computed tomography, the magnetic resonance imaging, and microcomputed tomography. This review examines the use of nanotechnologies for stem cell tracking, the many contrast agents, and detectors that have been proposed and suggest future directions for mouse to human translation of these techniques, for both therapeutic and diagnostic purposes.