The infusion of autologous stem cells has recently been put forward as an alternative strategy to regenerate infarcted myocardium and restore the contractile functions of diseased hearts. A growing number of cell types have been probed to induce cardiac repair in several animal models of ischemic myocardium, including human cardiac progenitor cells (hCPCs), human embryonic stem cells (hESCs), human mesenchymal stem cells (hMSCs) and human endothelial progenitor cells (hEPCs). The enthusiasm raised by pre-clinical studies has been dampened by clinical practice, according to which the extent of cardiac repair by cell based therapy is inadequate with respect to animal models. There is no doubt that regenerative medicine of acute myocardial infarction (AMI) will greatly benefit from the full comprehension of the signal transduction pathways which guide stem cell towards the injury site and their subsequent acquisition of a therapeutically relevant phenotype. The present review will focus on the role that oscillations in intracellular Ca2+ concentration might play to promote the stem cells-dependent regrowth of ischemic myocardium. We will describe how intracellular Ca2+ spikes may be manipulated to redirect stem cell fate to the most suitable lineage to restore cardiac vascularisation and contractility.