About 3% of newborns have a "major physical anomaly", meaning a physical anomaly that has cosmetic or functional significance.
The cause of 40-60% of congenital anomalies in humans is unknown.For 20-25% of anomalies there seems to be a "multifactorial" cause, meaning a complex interaction of multiple minor genetic anomalies with environmental risk factors. Another 10-13% of anomalies have a purely environmental cause (e.g. infections, illness, or drug abuse in the mother). Only 12-25% of anomalies have a purely genetic cause. Of these, the majority are chromosomal anomalies.
Genetic causes of congenital anomalies include inheritance of abnormal genes from the parents, as well as new mutations in one of the germ cells that gave rise to the fetus.
Environmental causes of congenital anomalies are referred to as teratogenic. These are generally problems with the mother's environment. Teratogens can include dietary deficiencies, toxins, or infections. For example, dietary deficiency of maternal folic acid is associated with spina bifida. Ingestion of harmful substances by the mother (e.g., alcohol, mercury, or prescription drugs such as phenytoin) can cause recognizable combinations of birth defects.
A limb anomaly is called a dysmelia. These include all forms of limbs anomalies, such as amelia, ectrodactyly, phocomelia, polymelia, polydactyly, syndactyly, polysyndactyly, oligodactyly, brachydactyly, achondroplasia, congenital aplasia or hypoplasia, amniotic band syndrome, and cleidocranial dysostosis.
Congenital anomalies of the heart include patent ductus arteriosus, atrial septal defect, ventricular septal defect, and tetralogy of fallot. Helen Taussig has been a major force in research on congenital anomalies of the heart.Congenital anomalies of the nervous system include neural tube defects such as spina bifida, meningocele, meningomyelocele, encephalocele and anencephaly. Other congenital anomalies of the nervous system include the Arnold-Chiari malformation, the Dandy-Walker malformation, hydrocephalus, microencephaly, megencephaly, lissencephaly, polymicrogyria, holoprosencephaly, and agenesis of the corpus callosum.
Congenital anomalies of the gastrointestinal system include numerous forms of stenosis and atresia, and imperforate.