Cardiac septation defects are among the most common birth defects in humans. The frequency of these defects reflects the complexity of cardiogenesis, which involves such processes as cell proliferation, migration, differentiation, and morphogenetic interactions. Major advances in the understanding of the underlying genetic etiologies of cardiac septation defects have provided insight into the genetic pathways involved. These genetic factors are most often transcription factors involved in the early stages of cardiogenesis. The ability to modify these genes in animal models is providing a better understanding of the role of these genes in common pathways leading to diverse forms of cardiac defects. Ultimately, our understanding of these basic processes should lead to molecular-based treatment and prevention options for those individuals most at risk for such birth defects.