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In the past 15 years, despite that regenerative medicine has shown great potential for cardiovascular diseases, the outcome and safety of stem cell transplantation has shown controversial results in the published literature. Medical imaging might be useful for monitoring and quantifying transplanted cells within the heart and to serially characterize the effects of stem cell therapy of the myocardium. From the multiple available noninvasive imaging techniques, magnetic resonance imaging and nuclear imaging by positron (PET) or single photon emission computer tomography (SPECT) are the most used clinical approaches to follow the fate of transplanted stem cells in vivo. In this article, we provide a review on the role of different noninvasive imaging modalities and discuss their advantages and disadvantages. We focus on the different in-vivo labeling and reporter gene imaging strategies for stem cell tracking as well as the concept and reliability to use imaging parameters as noninvasive surrogate endpoints for the evaluation of the post-therapeutic outcome.Labeling strategies for stem cell imaging. In vitro labeling strategies including PET with 18F-FDG (a glucose analog, which is taken up through the glucose transporter type 1 (GLUT1) into cell), SPECT with 111In-oxine or 99mTc-HMPAO (via passive diffusion into the cell) or MRI with SPIOs coated with transfection agents (allowing SPIOs stably maintained in cellular endosomes). Reporter gene imaging is based on reporter genes (vectors) transduced into stem cells, and followed by translation of mRNA and encoding to reporter protein, which processes specific affinity to an imaging reporter probe. Transplanted cells can be detected using PET, SPECT or MRI reporter probes.