Clinical and basic scientific studies of stem cell-based therapies have shown promising results for cardiovascular diseases. Despite a rapid transition from animal studies to clinical trials, the mechanisms by which stem cells improve heart function are yet to be fully elucidated. To optimize cell therapies in patients will require a noninvasive means to evaluate cell survival, biodistribution and fate in the same subject over time. Cell labeling offers the ability to image distinct cell lineages in vivo and investigate the efficacy of these therapies using standard noninvasive imaging techniques. In this article, we will discuss the most promising cell labeling techniques for translation to clinical cardiovascular applications.