Congenital heart disease has many diverse causes. Some factors are environmental, such as chemicals, drugs, or infection. However, the bulk of congenital heart disease is thought to be genetic in nature. Infections such as German measles (i.e. rubella) can produce congenital heart disease. Women with diabetes and phenylketonuria are at high risk for their children to be born with this disease. Other causes include the mother's excessive intake of alcohol and illegal drugs while pregnant. There are many genetic conditions which can be a factor in causing congenital heart disease, such as DiGeorge syndrome (22q11 deletion syndrome), Holt-Oram syndrome, and Alagille syndrome. Although these factors are known causes of congenital heart disease, most are currently unknown. Therefore, most cases of congenital heart disease are unknown.
Doctors do not know what causes most cases of congenital heart defects. Heredity may play a role. Inrare cases, more than one child in a family is born with a heart defect. Also, parents who have a congenital heart defect may be more likely than other parents to have a child with the condition. Babies who have certain other birth defects, such as Down syndrome, are also more likely to have congenital heart defects.
Other factors that raise the risk for congenital heart defects are:
Having viral infections, such as German measles (rubella), during pregnancy
Having diabetes
Taking some types of prescription or over-the-counter medicines during pregnancy
Being repeatedly exposed to some chemicals or x rays during pregnancy
Using alcohol or street drugs during pregnancy
Source http://www.wikipedia.org & http://www.nhlbi.nih.gov/