Molecular cardiology is a new and fast-growing area of cardiovascular medicine that aims to apply molecular biology techniques for the mechanistic investigation, diagnosis, prevention and treatment of cardiovascular disease. As an emerging discipline, it has changed conceptual thinking of cardiovascular development, disease etiology and pathophysiology. Although molecular cardiology is still at a very early stage, it has opened a promising avenue for understanding and controlling cardiovascular disease. With the rapid development and application of molecular biology techniques, scientists and clinicians are closer to curing heart diseases that were thought to be incurable 20 years ago. There clearly is a need for a more thorough understanding of the molecular mechanisms of cardiovascular diseases to promote the advancement of stem cell therapy and gene therapy for heart diseases. The present paper briefly reviews the state-of-the-art techniques in the following areas of molecular cardiology: gene analysis in the diseased heart; transgenic techniques in cardiac research; gene transfer and gene therapy for cardiovascular disease; and stem cell therapy for cardiovascular disease.