Stem cell therapy has emerged as a potential therapeutic option for cell death-related heart diseases. Preclinical and a number of early phase human studies suggested that cell therapy may augment perfusion and increase myocardial contractility. The rapid translation into clinical trials has left many issues unresolved, and emphasizes the need for specific techniques to visualize the mechanisms involved. Furthermore, the clinical efficacy of cell therapy remains to be proven. Imaging allows for in vivo tracking of cells and can provide a better understanding in the evaluation of the functional effects of cell-based therapies. In this review, a summary of the most promising imaging techniques for cell tracking is provided. Among these are direct labeling of cells with super-paramagnetic agents, radionuclides, and the use of reporter genes for imaging of transplanted cells. In addition, a comprehensive summary is provided of the currently available studies investigating a cell therapy-related effect on left ventricular function, myocardial perfusion, scar tissue, and myocardial viability.