Abstract: Ischemic heart disease (IHD) is the leading cause of death worldwide. Stem cell (SC)-based therapy has shown great potentials as a treatment. Nevertheless, research results are not as promising as expected and many questions remain to be investigated such as SC monitoring and survival in vivo. The emergence and development of molecular imaging provides approaches to solve these problems via long-term tracking of the transplanted cells. In this article we reviewed the changes and breakthroughs in molecular imaging from three aspects: monitoring of SCs survival, assessment of SC function in vivo and safety of SC-based therapy. Finally, we express expectations for the future utility of molecular imaging.