How do health care providers diagnose congenital anomalies?

Diagnosis of congenital anomalies depends on the specific problem and parts or systems of the body that are affected.

Many structural problems, such as club foot or cleft palate, are detected and diagnosed after a physical examination of the baby immediately after birth. For other conditions, newborn screening or prenatal testing is the only way to detect and diagnose problems.

This information focuses on structural congenital anomalies, their causes, their prevention, and their treatments. Functional/developmental congenital anomalies are addressed more completely in the intellectual and developmental disabilities content and in condition-specific topics.

Newborn Screening

Newborn screening, a process that tests infants' blood for different health conditions, including many congenital anomalies, provides one method of detecting problems. Newborn screening does not diagnose any specific conditions but detects that a problem may exist. By detecting problems immediately after birth, conditions can be diagnosed and treated before they have lifelong effects.

In addition, newborn screening routinely includes test for hearing problems, as well as pulse oximetry (test of baby's pulse rate and blood oxygen levels) to detect critical congenital heart defects.1

Infants who are at high risk for certain conditions—for example, because of their family history—can undergo additional testing at birth to detect these conditions and treat them if needed. This type of screening has been effective in detecting some cases of Menkes disease, allowing for treatment to begin before health problems occur.

Prenatal Screening

During pregnancy, pregnant people have routine tests, such as blood and urine tests, to check for diabetes, signs of infection, or disorders of pregnancy such as preeclampsia. Blood tests also measure the levels of certain substances in a pregnant person’s blood that determine the risk of the fetus for certain chromosomal disorders and neural tube defects. Ultrasound screenings, creating a picture using sound, allow providers to view the developing fetus in the womb. Some congenital anomalies, such as spina bifida, are detectable on ultrasounds.

Health care providers recommend that certain pregnant people, including those who are older than 35 years of age and those with a family history of certain conditions, get additional prenatal tests to screen for congenital anomalies. Prenatal detection allows doctors to start treatment as early as possible for some congenital anomalies.

Noninvasive prenatal testing (NIPT)2,3

NIPT is not a routine prenatal test but is used when a routine test suggests that the fetus may have a chromosomal disorder, such as having an extra or missing chromosome in each cell, which occurs in disorders such as Down syndrome, Patau syndrome, and Edwards syndrome.

NIPT analyzes the placental DNA present in the mother's blood; it does not require cell samples from inside the womb.

Currently, experts recommend NIPT only for high-risk pregnancies.4 This method does not detect open neural tube defects, nor does it predict late pregnancy complications.


Amniocentesis is a test that is usually performed to determine whether a fetus has a genetic disorder. In this test, a health care provider takes a small amount of fluid from the womb using a long needle. The fluid, called amniotic fluid, contains cells that have genetic material that is the same as the fetus's genetic material. A laboratory grows the cells and then examines their genetic material for any problems. Some congenital anomalies that can be detected with amniocentesis are Down syndrome and certain types of muscular dystrophy.

There is a slight risk of pregnancy loss with amniocentesis, so pregnant people should discuss the procedure with their health care provider before making a decision about the test.

Chorionic Villus Sampling (CVS)6,7

This test extracts cells from inside the womb to determine whether the fetus has a genetic disorder. Using a long needle, the health care provider takes cells from the chorionic villi, which are tissues in the placenta, the organ in the womb that nourishes the fetus. The genetic material in the chorionic villus cells is identical to that of the fetal cells.

Like amniocentesis, CVS can be used to test for chromosomal disorders and other genetic problems. CVS can be done earlier in pregnancy than amniocentesis, but it is also associated with a slightly higher risk of miscarriage than amniocentesis. Pregnant people who are considering CVS should discuss the test and the risks with their health care provider.

Links to more information about prenatal testing are available in the Resources section of this topic.


  1. Centers for Disease Control and Prevention. (2012). Pulse oximetry screening for critical congenital heart defects. Retrieved July 26, 2017, from
  2. Thompson, A. E. (2015). Noninvasive prenatal testing. JAMA, 314(2), 198. Retrieved February 7, 2017, from external link
  3. Gregg, A. R., Skotko, B. G., Benkendorf, J. L., Monaghan, K. G., Bajaj, K., Best, R. G., et al. (2016). Noninvasive prenatal screening for fetal aneuploidy, 2016 update: A position statement of the American College of Medical Genetics and Genomics. Genetics in Medicine, 18, 1056–1065. Retrieved February 7, 2017, from external link (PDF 323 KB)
  4. Society for Maternal-Fetal Medicine. (2014). SMFM statement: Maternal serum cell-free DNA screening in low risk women. Retrieved April 21, 2017, from
  5. National Library of Medicine. (2015). Amniocentesis. Retrieved on February 7, 2017, from
  6. Simpson, J. L., & Otano, L. (2007). Prenatal genetic diagnosis. In S. G. Gabbe, J. R. Niebyl, & J. L. Simpson (Eds.), Obstetrics: Normal and problem pregnancies (5th ed.). New York, NY: Churchill Livingstone.
  7. American College of Obstetricians and Gynecologists. (2016). Practice bulletin no. 162: Prenatal diagnostic testing for genetic disorders Obstetrics & Gynecology, 127(5), e108–e122.
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