Cardiac stem cell therapy is an innovative and promising therapeutic approach for heart failure. However, despite an increasing body of existing experimental and human data, it still presents a substantial challenge for basic scientists and clinical researchers. Several issues concerning biologic mechanisms of therapy remain to be answered, and unequivocal proof of clinical efficacy is needed. The variety of different available cell types and different methods for cell delivery to the myocardium raises further questions about the most useful therapeutic approach. Nuclear imaging not only provides accurate noninvasive information about myocardial perfusion, contractile function and viability, which enables assessment of clinical benefits of therapy. The rapidly developing field of molecular imaging has also brought up more specific tracers targeting cellular and subcellular biologic events, which are expected to shed more light upon mechanisms of cell therapy. Moreover, nuclear imaging is well suited for tracking of transplanted cells by use of direct radionuclide labeling or genetic labeling with reporter genes that can be targeted by radioactive reporter probes. Such a broad spectrum of available in vivo information is expected to significantly impact the future development of cell therapy towards a clinically accepted treatment.