What causes congenital anomalies?

Different congenital anomalies have different causes, and the causes of many congenital anomalies remain unknown.

A specific condition might be caused by one or more of the following primary problems:¹

• Genetic problems. One or more genes might have a change or mutation that results in them not working properly, such as in Fragile X syndrome. Similarly, a gene or part of the gene might be missing.
• Chromosomal problems. In some cases, a chromosome or part of a chromosome might be missing, such as in Turner syndrome, when a female is missing an X chromosome. Other congenital anomalies result from having an extra chromosome, such as in Klinefelter syndrome and Down syndrome.
• Infections. Women who get certain infections during pregnancy are at higher risk for having a child with birth defects. For example, infection with Zika virus during pregnancy is linked with the congenital anomaly called microcephaly, in which the brain and skull are atypically small. Zika infection in pregnancy is linked to other structural problems with the brain as well. Our Pregnancy topic has more information on infections that can cause congenital anomalies and other problems in newborns and on ways to prevent them during pregnancy, and CDC provides tips for preventing infections before and during pregnancy.
• Exposure to medications, chemicals, or other agents during pregnancy. The infants whose mothers took thalidomide are examples of an exposure leading to congenital anomalies. Other examples include exposure to rubella (also called German measles) and toxic chemicals, such as hydrocarbons.²