Mesenchymal stem cells (MSCs) exhibit multipotent differentiation potential and can be derived from embryonic, neonatal and adult differentiation stage III tissue sources. While increasing preclinical studies and clinical trials have indicated that MSC-based therapy is a promising strategy for cardiovascular regeneration, there are major challenges to overcome before this stem-cell technology can be widely applied in clinical settings. In this review, the following important issues will be addressed. First, optimal sources of MSC derivation suitable for myocardial repair are not determined. Second, assessments for preclinical and clinical studies of MSCs require more scientific data analysis. Third, mechanisms of MSC-based therapy for cardiovascular regeneration have not been fully understood yet. Finally, the potential benefit-risk ratio of MSC therapy needs to be evaluated systematically. Additionally, future development of MSC therapy will be discussed.