Neural tube defects (NTDs) are among the most common complex congenital malformations observed in newborns. When the neural tube fails to close completely, severe malformations of the brain and/or spinal cord and subsequent neurologic impairment occurs. It is widely believed that nutritional, environmental and genetic interactions contribute to NTDs. It is well established that low folate levels during pregnancy increases a mother's risk of having pregnancy complicated by an NTD, and providing periconceptional folate supplementation reduces this risk. The underlying genetic mechanisms of NTDs are still unclear. We review the many new approaches to better understand the etiology, especially the genetic etiology, underlying this family of birth defects.