The heart is the first organ to form and function in the embryo, and all subsequent events in the life of the organism depend on the heart's ability to match its output with the organism's demands for oxygen and nutrients. Abnormalities in heart formation, the most common form of human birth defects, afflict nearly 1% of newborns, and their frequency in spontaneously aborted pregnancies is estimated to be tenfold higher. With the completion of the sequencing of the human genome, molecular genetic efforts directed at finding genes for monogenic traits have accelerated dramatically. Breakthroughs in molecular genetic technology have just begun to be applied in pediatric cardiology stemming from the use of chromosomal mapping and the identification of genes involved in both the primary etiology and as significant risk factors in the development of cardiac and vascular abnormalities. This review will focus on information provided by molecular and genetic analysis in the diagnosis, treatment and overall heart disorders.