Currently, the tenet that heart muscle cells are terminally differentiated and incapable of self-repair is being challenged. Recent experimental observations suggest that both endogenous and exogenous stem cell populations have the potential to regenerate damaged areas within the heart. These findings hold promise for new therapeutic strategies to treat cardiovascular diseases, including common conditions like myocardial infarction and transplant vascular disease (TVD). In this chapter, we focus on the study of endogenous stem cells in the context of their role in modulation of cardiovascular diseases, including ischemic heart disease and TVD. Specific experimental models and methods used to study the phenomena of endogenous bone marrow-derived stem cell migration and potential differentiation are also described.