It is unclear why atrial septal defects occur, but some congenital heart defects appear to be familial and are sometimes accompanied by other genetic problems, such as Down syndrome. In addition, certain conditions that occur during pregnancy can increase the risk of a fetus having an atrial septal defect, including: 1. Rubella virus infection: Infection with rubella, such as German measles, during the first few months of pregnancy increases the risk of the fetus having a heart defect. 2. drug, tobacco or alcohol use, or exposure to certain substances: using certain drugs, smoking, drinking or drugs such as cocaine during pregnancy can harm a developing fetus. 3. Diabetes or lupus: Having diabetes or lupus may contribute to the risk of heart defects in the fetus. Atrial septal defects can be caused by a combination of genetic and environmental factors. Patients with a definite diagnosis of atrial septal defects should seek further medical attention.