The heart is an organ with special significance in medicine and developmental biology. The development of the heart and its vessels during embryogenesis is the result of numerous and complex processes. At present, our understanding is based on decades of meticulous anatomical studies. However, the spectacular progress of modern molecular biology and developmental biology has marked the beginning of a new era in embryology. The molecular bases for cardiogenesis are just emerging. Several families of genes with restricted expression to the heart have been identified in the last years, including genes encoding for contractile proteins, ion channels as well as transcription factors involved in tissue specific gene expression. Likewise, the analyses of regulatory elements have increased our understanding of the molecular mechanisms directing gene expression. In this review, we illustrate the different patterns of gene and transgene expression in the developing myocardium. These data demonstrate that the wide molecular heterogeneity observed in the developing myocardium is not restricted to embryogenesis but it also remains in the adulthood. Therefore, such molecular diversity should be taken into account on the design of future gene therapy approaches, having thus direct clinical implications.