While certain types of congenital heart disease may be diagnosed in-utero, the reason for their developing in the first place is frequently unknown. In general, women are urged to avoid exposure to conditions such as infection and certain drugs. The U.S. Food and Drug Administration (FDA) recently issued a warning about the use of the drug Paxil by pregnant women. New studies suggest an increased risk of heart defects, particularly VSD, in women who use Paxil during pregnancy.

As genetic research advances, however, it is hoped that DNA testing will allow for early diagnosis (and, therefore, early treatment) for many types of septal defects. Genetic research continues to make progress in identifying proteins involved in heart structure and function, and how abnormal (mutated) forms of those proteins influence congenital heart defects. For example, scientists have uncovered mutations in genes responsible for a normal heart septum.