More children die from congenital heart defects (CHD) each year than are diagnosed with childhood cancer, yet the causes remain unknown. The remarkable conservation of genetic pathways regulating cardiac development in species ranging from flies to humans provides an opportunity to experimentally dissect the role of critical cardiogenic factors. Utilization of model biological systems has resulted in a molecular framework in which to consider the etiology of CHD. As whole genome sequencing and single nucleotide polymorphism data become available, identification of genetic mutations predisposing to CHD may allow preventive measures by modulation of secondary genetic or environmental factors. In this review, genetic pathways regulating cardiogenesis revealed by cross-species studies are reviewed and correlated with human CHD.