In the mid-1980s, iron oxide nanoparticles were developed as contrast agents for diagnostic imaging. In the last two decades, established methods to label cells with superparamagnetic iron oxides (SPIOs) have been developed to aid in targeted delivery and tracking of stem cell therapies. The surge in cellular therapy clinical trials for cardiovascular applications has seen a similar rise in the number of preclinical animal studies of SPIO-labeled stem cells in an effort to understand the mechanisms of cardiovascular regenerative therapy and stem cell biodistribution. The adoption of a limited number of methods of direct labeling of stem cells with SPIOs is due in large part to the desire to rapidly translate these techniques to clinical trials. In this review, we will outline the most commonly adopted methods for iron oxide labeling of stem cells for cardiovascular applications and describe strategies for magnetic resonance imaging (MRI) of magnetically labeled cells in the heart.