Although approximately 50% of all congenital anomalies cannot be linked to a specific cause, some known genetic, environmental, and other causes or risk factors are known.

1.   Genetic factors

Genes play an essential role in many congenital anomalies. This might be through inherited genes that code for an anomaly or resulting from sudden changes in genes known as mutations.

Consanguinity (when parents are related by blood) also increases the prevalence of rare genetic congenital anomalies and nearly doubles the risk for neonatal and childhood death, intellectual disability, and other anomalies.

Some ethnic communities (such as Ashkenazi Jews or Finns) have a comparatively high prevalence of rare genetic mutations such as Cystic Fibrosis and Haemophilia C.

2.   Socioeconomic and demographic factors

Low-income may be an indirect determinant of congenital anomalies, with a higher frequency among resource-constrained families and countries. It is estimated that about 94% of severe congenital anomalies occur in low- and middle-income countries. An indirect determinant, this higher risk relates to a possible lack of access to sufficient, nutritious foods by pregnant women, an increased exposure to agents or factors such as infection and alcohol, or poorer access to healthcare and screening. Factors often associated with lower-income may induce or increase the incidence of abnormal prenatal development.

Maternal age is also a risk factor for abnormal intrauterine fetal development. Advanced maternal age increases the risk of chromosomal abnormalities, including Down syndrome.

3.   Environmental factors

Maternal exposure to certain pesticides and other chemicals and certain medications, alcohol, tobacco and radiation during pregnancy may increase the risk of having a fetus or neonate affected by congenital anomalies. Working or living near, or in, waste sites, smelters or mines may also be a risk factor, particularly if the mother is exposed to other environmental risk factors or nutritional deficiencies.

4.   Infections

Maternal infections such as syphilis and rubella are a significant cause of congenital anomalies in low- and middle-income countries.

Zika virus infection during pregnancy is a cause of microcephaly and other congenital abnormalities in the developing fetus and newborn. Zika infection in pregnancy also results in pregnancy complications such as fetal loss, stillbirth, and preterm birth.  

5.   Maternal nutritional status

Maternal folate insufficiency increases the risk of having a baby with a neural tube defect, while excessive vitamin A intake may affect an embryo or fetus normal development.

Preventive public health measures work to decrease the frequency of specific congenital anomalies by removing risk factors or the reinforcement of protective factors. Necessary interventions and efforts include:

ensuring adolescent girls and mothers have a healthy diet including a wide variety of vegetables and fruit, and maintain a healthy weight;
ensuring an adequate dietary intake of vitamins and minerals, and particularly folic acid in adolescent girls and mothers;
ensuring mothers avoid harmful substances, particularly alcohol and tobacco;
avoidance of travel by pregnant women (and sometimes women of child-bearing age) to regions experiencing outbreaks of infections known to be associated with congenital anomalies;
reducing or eliminating environmental exposure to hazardous substances (such as heavy metals or pesticides) during pregnancy;
controlling diabetes before and during pregnancy through counseling, weight management, diet, and administration of insulin when required;
ensuring that any exposure of pregnant women to medications or medical radiation (such as imaging rays) is justified and based on careful health risk-benefit analysis;
vaccination, especially against the rubella virus, for children and women;
increasing and strengthening the education of health staff and others involved in promoting prevention of congenital anomalies;
screening for infections, especially rubella, varicella, and syphilis, and consideration of treatment.

Health care before and around the time of conception (preconception and peri-conception) includes basic reproductive health practices and medical genetic screening and counseling. Screening can be conducted during the 3 periods listed:

Preconception screening can be helpful to to identify those at risk for specific disorders or at risk of passing a disorder onto their children. Screening includes obtaining family histories and carrier screening and is particularly valuable in countries where consanguineous marriage is common.
Peri-conception screening: maternal characteristics may increase risk, and screening results should be used to offer appropriate care, according to risk. This may include screening for young or advanced maternal age, as well as screening for use of alcohol, tobacco or other risks. Ultrasound can be used to screen for Down syndrome and major structural abnormalities during the first trimester, and for severe fetal anomalies during the second trimester. Maternal blood can be screened for placental markers to aid in prediction of risk of chromosomal abnormalities or neural tube defects, or for free fetal DNA to screen for many chromosomal abnormalities. Diagnostic tests such as chorionic villus sampling and amniocentesis can be used to diagnose chromosomal abnormalities and infections in women at high risk.
Neonatal screening includes clinical examination and screening for disorders of the blood, metabolism and hormone production. Screening for deafness and heart defects, as well as early detection of congenital anomalies, can facilitate life-saving treatments and prevent progression towards some physical, intellectual, visual, or auditory disabilities. In some countries, babies are routinely screened for abnormalities of the thyroid or adrenal glands before discharge from the maternity unit.

Many structural congenital anomalies can be corrected with pediatric surgery, and early treatment can be administered to children with functional problems such as thalassemia (inherited recessive blood disorders), sickle cell disorders, and congenital hypothyroidism (reduced function of the thyroid).