Stem cells have a potential to dramatically change the common modalities of treatment for many diseases. Despite their rapid transition from animal studies to clinical applications, a number of unanswered questions remain regarding in vivo behaviors of stem cells transplanted into target tissues, including questions about their survival, distribution, migration, differentiation, and tumorigenicity. Recent advances in noninvasive molecular imaging technologies, including optical imaging, magnetic resonance imaging (MRI), radionuclide imaging, and reporter genebased imaging, have gradually elucidated the fundamental behaviors of stem cells via in vivo real time qualitative and quantitative monitoring. Here, we briefly review current imaging techniques for tracking stem cells, with an emphasis on the advantages and drawbacks of each imaging approach, and discuss future prospects for in vivo tracking of stem cells in regenerative medicine.