Intra-myocardial and intra-coronary transplantation of somatic stem cells as a therapy of heart failure is currently under clinical evaluation. A major limitation of all clinical studies dealing with myocardial cell engraftment is the inability to track the fate of the transplanted cells. This would be crucial for the scientific interpretation and monitoring of possible contribution of engrafted cells to improved cardiac function. We present an overview of all publications focusing on promising novel technologies that may allow for short- and long-term follow up of transplanted cells by visualization. Clinicians should consider appropriate bioimaging methods for in vivo visualization of engrafted cells in the heart when designing clinical studies.