Australian Institute of Health and Welfare (2022) Congenital anomalies 2016, AIHW, Australian Government, accessed 04 July 2022.
Australian Institute of Health and Welfare. (2022). Congenital anomalies 2016. Retrieved from https://www.aihw.gov.au/reports/mothers-babies/congenital-anomalies-in-australia-2016
Congenital anomalies 2016. Australian Institute of Health and Welfare, 01 April 2022, https://www.aihw.gov.au/reports/mothers-babies/congenital-anomalies-in-australia-2016
Australian Institute of Health and Welfare. Congenital anomalies 2016 [Internet]. Canberra: Australian Institute of Health and Welfare, 2022 [cited 2022 Jul. 4]. Available from: https://www.aihw.gov.au/reports/mothers-babies/congenital-anomalies-in-australia-2016
Australian Institute of Health and Welfare (AIHW) 2022, Congenital anomalies 2016, viewed 4 July 2022, https://www.aihw.gov.au/reports/mothers-babies/congenital-anomalies-in-australia-2016
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Descriptions of the anomalies included in this report are outlined below. These were developed in consultation with the NCAAG and clinical experts using a range of information sources.
Trisomy 21 (Down syndrome)
Trisomy 21, otherwise known as Down syndrome, is a chromosomal anomaly in which there is an excess of chromosome 21 material. In most cases this is due to an extra copy of chromosome 21 in each cell (trisomic Down syndrome); less frequently it is due to an extra copy of chromosome 21 being present in only some cells (mosaic Down syndrome) or a piece of an extra copy of chromosome 21 being attached to another chromosome (translocation Down syndrome). Down syndrome varies in severity causing intellectual disability and developmental delays. It is the most common genetic chromosomal disorder and cause of learning disabilities in children. Babies born with Down syndrome will usually have other anomalies.
Trisomy 18 (Edwards syndrome)
Trisomy 18, otherwise known as Edwards syndrome, is a chromosomal anomaly in which there is an excess of chromosome 18 material. In most cases this is due to an extra copy of chromosome 18 in each cell (trisomic Edwards syndrome); less frequently it is due to an extra copy of chromosome 18 being present in only some cells (mosaic Edwards syndrome) or a piece of an extra copy of chromosome 18 being attached to another chromosome (translocation Edwards syndrome). Babies with Edwards syndrome are usually small at birth due to intrauterine growth delay and may be stillborn; most liveborn babies with Edwards syndrome have a limited life expectancy. All babies with Edwards syndrome have learning disabilities and may have other anomalies.
Trisomy 13 (Patau syndrome)
Trisomy 13, otherwise known as Patau syndrome, is a chromosomal anomaly in which there is an excess of chromosome 13 material. In most cases this is due to an extra copy of chromosome 13 in each cell (trisomic Patau syndrome); less frequently it is due to an extra copy of chromosome 13 being present in only some cells (mosaic Patau syndrome) or a piece of an extra copy of chromosome 13 being attached to another chromosome (translocation Patau syndrome). Patau syndrome babies may miscarry, be stillborn or be small for gestational age due to intrauterine growth restriction, and for liveborn babies it is a life-limiting condition. All babies with Patau syndrome have a range of cardiac, central nervous system and skeletal anomalies.
Female sex chromosome anomalies (including Turner syndrome)
Turner syndrome is a female only chromosomal congenital anomaly. The cause is either a missing X-chromosome (monosomic 45, X) or a chromosomal rearrangement involving the X chromosome (translocation Turner syndrome). The chromosomal anomaly may only be present in some cells (mosaic Turner syndrome). Women with Turner syndrome are short in stature and many have non-functioning ovaries leading to an absence of periods, infertility and premature menopause.
Male sex chromosome anomalies (including Klinefelter syndrome)
Klinefelter syndrome is a male only chromosomal congenital anomaly in which there is an extra copy of the X chromosome (47, XXY). Men with Klinefelter syndrome may not present any symptoms, though learning and behavioural disorders and infertility are common.
Other chromosomal anomalies include:
Includes anomalies related to the addition to, absence of and rearrangement of chromosomes. Humans have 23 pairs of chromosomes (thread-like structures in the nucleus of cells).
Transposition of the great vessels
Transposition of the great vessels is an anomaly where the 2 main arteries carrying blood out of the heart—the pulmonary artery and the aorta—are switched in position. This means oxygen-poor blood is circulated to the body instead of the lungs and oxygen-rich blood returns to the lungs instead of the body. It is considered a critical congenital heart defect because a baby with this anomaly will need surgery or other procedures soon after birth.
Cardiac septal anomalies
Cardiac septal anomalies are a group of heart conditions in which there is a hole in the wall that divides the chambers of the heart. This includes:
Many of these holes are found by chance and never cause any concerns. Small holes may close on their own and medium to large holes may need surgical closure during childhood.
Atrial septal defect
An atrial septal defect is an anomaly in which there is a hole in the wall that separates the 2 upper chambers (right and left atria) of the heart. Before birth this opening allows blood to detour away from the lungs. After birth the opening is no longer needed and closes or becomes very small within several weeks or months. An atrial septal defect results when the opening is larger than normal and does not close after birth. Small defects may be found by chance, may never cause a problem and close during infancy or early childhood. Large defects may require surgical closure later in life.
Atrioventricular septal defect
An atrioventricular septal defect is an anomaly in which there is a hole in the centre of the heart and the valves (mitral and tricuspid) which control the blood flow between the chambers may not have developed typically. This leads to blood flowing back through the hole from the left chamber (which normally pumps blood only to the body) to the right chamber and into the lungs, which causes the lungs and heart to work harder than they should. These defects can be classified into 3 categories: complete, partial (or incomplete) and transitional. Babies born with an atrioventricular septal defect require surgery and may have life-long complications. With regular follow-up and treatment, most grow up to lead healthy lives.
Ventricular septal defect
A ventricular septal defect is a hole in the wall that separates the 2 lower chambers of the heart (right and left ventricles). This means that oxygen-rich blood passes from the left lower chamber through the hole where it mixes with oxygen-poor blood in the right lower chamber. Large defects may need surgical repair early in life to prevent complications. Small defects may not cause problems and close on their own.
Other cardiac septal defects
Includes other cardiac septal defects not already specified.
Tetralogy of Fallot
Tetralogy of Fallot is an anomaly in which 4 cardiac malformations are present:
As a result, oxygen-poor blood is returned to the body rather than the lungs.
Tetralogy of Fallot may be associated with a chromosomal anomaly. It is considered a critical congenital heart defect as a baby will need surgery or other procedures soon after birth.
Pulmonary valve atresia
Pulmonary valve atresia is an anomaly in which the pulmonary valve is not formed, so blood cannot get from the right ventricle of the heart to the lungs via the pulmonary artery. Blood must use other routes to bypass the unformed pulmonary valve to allow the oxygenation of the blood. This anomaly is considered a critical congenital heart defect because a baby may need surgery or other procedures soon after birth.
Hypoplastic left heart syndrome
Hypoplastic left heart syndrome is an anomaly in which a number of structures on the left side of the heart are underdeveloped, including the left ventricle, the mitral valve, the aortic valve and the ascending portion of the aorta. Babies with hypoplastic left heart syndrome frequently also have an atrial septal defect. This means the left side of the heart cannot pump oxygen-rich blood to the body properly. This anomaly is considered a critical congenital heart defect because a baby may need surgery or other procedures soon after birth.
Patent ductus arteriosus
Patent ductus arteriosus is an anomaly in which a vascular connection between the aorta and the pulmonary artery persists after a baby is born. During pregnancy, this connection allows blood to bypass circulation to the lungs. After birth, blood must receive oxygen in the lungs and the connection should close. This anomaly results when the hole remains open and blood may skip oxygenation. If left untreated, it can result in pulmonary hypertension and heart failure. It can be treated with surgery or other procedures.
Coarctation of aorta
Coarctation of aorta is an anomaly in which a segment of the aorta (the main artery leaving the heart to supply blood to the body) is narrowed and the blood which typically flows through the aorta is obstructed. It is indicated by weak pulses in the legs or groin and a heart flow murmur found by examination of the baby. If severe, the heart must work harder and high blood pressure and heart failure may result, though symptoms may not appear for some time. Coarctation of aorta often occurs with other cardiac anomalies and may require surgery.
Other circulatory system
Other circulatory system anomalies include anomalies of the:
Any circulatory system
Includes anomalies of the circulatory system, i.e. the heart and the major blood vessels. The circulatory system (often called the cardiovascular system) is the system that allows blood containing oxygen and nutrients to reach the cells and tissues.
Cleft lip and/or palate
Cleft lip and/or palate is an anomaly characterised by partial or complete splitting of the upper lip, with or without splitting of the hard palate behind the upper front teeth. Babies with cleft lip and/or palate often have challenges with feeding, hearing and speech. Treatment depends on the severity of the cleft and surgery may be required.
Tracheo-oesophageal fistula is an anomaly in which there is an atypical connection between the oesophagus and the trachea. Normally, the oesophagus and trachea are not connected. It may be associated with oesophageal atresia or the incomplete development of the oesophagus. When a baby with trachea-oesophageal fistula swallows, liquid can pass into the lungs resulting in symptoms such as frothy, white bubbles in the mouth, coughing and choking. Surgical closure of the fistula is often required to allow feeding and to avoid lung damage.
Anomalies leading to oesophageal obstruction (without fistula)
Anomalies which lead to a partial or complete blockage of the oesophagus, causing swallowing difficulties. These include:
Oesophageal atresia is an anomaly in which the lower end of the oesophagus is closed and does not connect with the stomach, and as such ends in a blind pouch. It is commonly diagnosed after birth when the baby first tries to feed and has choking or vomiting, or when a tube inserted in the baby’s nose or mouth cannot pass down into the stomach.
Oesophageal stenosis, stricture and web present with feeding difficulties in a baby and may not be obvious in the newborn.
Congenital hypertrophic pyloric stenosis
Congenital hypertrophic pyloric stenosis is an anomaly caused by the thickening of the lower part of the stomach which connects to the small intestine. This can lead to near complete obstruction of the digestive system preventing food from reaching the small intestine. Pyloric stenosis usually appears within 3 to 5 weeks after birth. It can lead to projectile vomiting, dehydration and weight loss and difficulty feeding. Surgery is required.
Atresia/stenosis of intestines
Atresia of the intestines occurs when there is a complete closure of the intestine. Stenosis is a partial obstruction which causes the opening of the intestine to become narrower. Intestinal atresia and stenosis generally occur at the small intestine but can occur at any point in the gastrointestinal tract. These obstructions prevent proper absorption of food and may lead to vomiting, dehydration, swelling of the abdomen and difficultly in putting on weight. Babies with intestinal atresia or stenosis will require surgery.
Hirschsprung disease is an anomaly characterised by the absence of the normal movement (peristalsis) in a segment of the bowel due to a lack of nerve supply in that section. As a result, the muscles in the bowel lose their ability to move the bowel contents through the intestine, leading to constipation and/or partial or complete bowel obstruction. Surgery is usually required.
Other digestive system
Other digestive system anomalies include anomalies of the:
Any digestive system
Includes anomalies of the mouth, oesophagus, stomach, intestines, liver and pancreas.
Eye, ear, face and neck and integuments
Anophthalmia and microphthalmia
Anophthalmia and microphthalmia are anomalies of the eye. Anophthalmia describes the absence of a recognisable eyeball and microphthalmia an unusually small eyeball. Both conditions may affect one or both eyes. These anomalies are frequently associated with other anomalies.
Microtia with congenital absence, atresia and stricture of external auditory canal
Microtia is characterised by a small and atypically shaped external ear. In most severe cases, the external ear may be absent. Microtia is often associated with the absence or narrowing of the external ear canal. These anomalies are frequently one-sided but may be two-sided and are often associated with other anomalies.
Other eye, ear, face and neck and the integuments
Other eye, ear, face and neck and integumentary system anomalies include anomalies of:
Any eye, ear, face and neck and the integuments
Includes anomalies of the eyes, the ears, the face and neck and the integumentary system (skin, hair, nails, sweat glands and breasts).
Doubling anomalies of the female genitalia
Doubling anomalies of the female genitalia are anomalies where there is a doubling of either the uterus (from a dimple in the top of the uterus to a completely double uterus) or other genital organs such as the vagina.
The uterus normally develops from the fusion of two cords of tissue (Mullerian ducts), and this group of anomalies occur when that fusion is incomplete. A duplicate uterus may or may not also develop duplicate cervixes and vaginas.
There may be no apparent symptoms or symptoms may become apparent during puberty and treatment, if required, may be undertaken in adulthood.
Hypospadias is an anomaly where the opening of the urethra is on the underside of the penis instead of at the tip. The urethra is the tube through which urine drains from the bladder and passes through the penis in a male. Hypospadias does not cause difficultly for an infant. Surgery is undertaken at 6 to 12 months of age and aims to restore the regular appearance of the penis and functions such as typical urination and reproduction.
Anomalies related to indeterminate sex
Congenital anomalies related to indeterminate sex are anomalies where there is ambiguity of a baby’s genitalia and the observable genital characteristics do not readily allow for sex determination at birth.
Other genital organs
Other genital organ anomalies include:
Any genital organs
Includes anomalies of the genital organs (those involved in human reproduction), including the uterus, ovaries, Fallopian tubes, cervix and vagina; penis, testes and scrotum.
Congenital hip dislocation
Congenital hip dislocation (otherwise known as developmental dysplasia of the hip) is an anomaly of the hip joint. The ball at the top of the femur is not stable within the hip socket as the socket of the hip is too shallow, and the ligaments of the hip joint that hold it together may also be loose. In severe cases, the femur may also dislocate. Congenital hip dislocation may affect one or both hips. It is usually treated by a brace or plaster case to position the baby’s hips correctly and surgery may be needed as the baby grows.
Talipes is a group of anomalies in which the position of the foot is not typical. In talipes equinovarus, the foot turns inward and the front half of the foot points down. In talipes calcaneovalgus, the foot is pushed up and the front half of the foot turns outwards. Talipes is treated by combinations of stretching, casting and bracing, and surgery.
Polydactyly is an anomaly where a baby is born with extra fingers or toes. It can affect the hand, the foot, or both and is usually treated surgically.
Syndactyly is an anomaly where a baby is born with webbed or conjoined digits (fingers and/or toes). It may occur in isolation or be part of an inherited syndrome. It is usually treated surgically.
Reduction defect of upper limb(s)
Reduction defect of upper limb(s) is an anomaly where a part of, or the entire arm (upper limb) does not form completely during pregnancy. This is referred to as a 'limb reduction' because a limb is reduced from its expected size or is missing. Treatment is individualised to each child as each anomaly causes unique challenges.
Reduction defect of lower limb(s)
Reduction defect of lower limb(s) is an anomaly where a part of, or the entire leg (lower limb) does not form completely during pregnancy. This is referred to as a 'limb reduction' because a limb is reduced from its expected size or is missing. Treatment is individualised to each child as each anomaly causes unique challenges.
Congenital diaphragmatic hernia
Congenital diaphragmatic hernia is an anomaly in which the diaphragm does not develop typically. The diaphragm usually separates the organs in the abdomen from those in the chest. Severity ranges from a thinned area in part of the diaphragm to its complete absence. It may allow the stomach and intestines to protrude into the chest cavity, crowding the heart and lungs. This can lead to the underdevelopment of the lungs. Congenital diaphragmatic hernia is a critical condition and requires surgery after birth.
Exomphalos (also known as Omphalocele), is an anomaly where there is incomplete development of the baby’s abdominal wall where it meets the umbilical cord. This leads to the intestine, and at times liver and bowel, protruding outside the abdomen in a sac surrounding the umbilical cord. A baby with exomphalos will require surgery after birth to place the organs within the abdominal cavity and close the abdominal wall.
Gastroschisis is an anomaly where an opening forms in the abdominal wall, generally at the right side of the joining of the umbilical cord. This leads to the bowel protruding outside the body and developing in the amniotic fluid, causing the intestines to become irritated, shortened, or swollen. Surgery is required after birth to place the organs inside the baby’s abdomen and to close the abdominal wall.
Other musculoskeletal system
Other musculoskeletal system anomalies include anomalies such as:
Includes any anomalies of the bones, muscles, tendons, ligaments and soft tissues.
Neural tube defects
Neural tube defects occur when brain and spinal development is disrupted. During gestation, a flat neural plate ‘rolls up’ into a tube to form the head and back. If the closure of the neural tube is incomplete, a neural tube defect results. A number of nervous system anomalies are grouped together as neural tube defects including:
Anencephaly and related anomalies
Anencephaly is an anomaly characterised by the total or partial absence of the cranial vault, the covering skin, and the brain is missing or reduced to a small mass. The related conditions of craniorachischisis, iniencephaly and acrania are included. Babies with anencephaly are usually either stillborn or die shortly after birth.
Encephalocele is an anomaly in which there is a sac-like protrusion of the brain and the membranes that cover it through an opening in the skull. It occurs when a portion of the developing skull fails to close properly (a ‘neural tube defect’). It is treated surgically by placing the protruding part of the brain and the membranes covering it back into the skull and closing the opening in the skull. It can cause long-term neurological complications and multiple surgical treatments may be necessary.
Spina bifida describes a group of anomalies in which the developing spinal cord does not develop or close properly (a ‘neural tube defect’). This leads to the exposure or protrusion of the spinal cord, with or without its coverings, through the spine. It is usually associated with a degree of paralysis or other nervous system dysfunction. Also includes Arnold-Chiari malformation, an anomaly in which part of the brain at the back of the skull bulges through the opening where the skull joins the spinal canal. This places pressure on part of the brain and spinal cord and can cause dizziness, muscle weakness, numbness, vision problems, headache and challenges with balance and coordination.
Microcephaly is an anomaly in which a baby’s head is significantly smaller than expected when compared to other babies of the same sex and gestational age. It occurs when a baby's brain has not developed typically during pregnancy and has been linked to a range of infections and exposure to harmful substances during pregnancy. It is associated with developmental delay and intellectual disability, seizures and difficulties with vision, hearing and feeding. It is a life-long condition with no known treatments or cure.
Congenital hydrocephalus is an anomaly where there is an excess of the fluid that surrounds and protects the brain and spinal cord. This increases pressure on the brain and causes brain injury and other outcomes. If left untreated, blindness and ongoing cognitive deterioration may occur. Surgical treatments are available to divert the cerebrospinal fluid to another part of the body to reduce pressure on the brain.
Other nervous system
Other nervous system anomalies include anomalies of the:
Any nervous system
Includes anomalies of the central nervous system (brain and spinal cord) and the peripheral nervous system (body nerves).
Hypoplasia and dysplasia of lung
Hypoplasia and dysplasia of the lung is an anomaly that occurs when lung tissue and airways are underdeveloped. If severe, lung function may be unable to sustain life. Pulmonary hypoplasia is often associated with other anomalies and the type of treatment will vary. Babies that survive will often have life-long lung issues. During pregnancy, pulmonary hypoplasia is frequently associated with a reduced volume of amniotic fluid surrounding the baby.
Other respiratory system anomalies include anomalies of the:
Includes anomalies of the respiratory system, i.e. the airways and lungs.
Renal agenesis is an anomaly where a baby is missing one or both kidneys and renal hypoplasia is where a baby has small and poorly functioning kidneys. Renal agenesis or hypoplasia is usually indicated by an insufficient amount of amniotic fluid during pregnancy which places pressure on the baby. In severe cases of reduced amniotic fluid, compression may lead to Potter syndrome. Potter syndrome refers to a group of features including a flattened nose, recessed chin, skin folds covering the corners of the eyes and low-set ears. Low amniotic fluid can also lead to underdeveloped lungs and severe breathing difficulties for the baby.
Cystic kidney disease
Cystic kidney disease is a group of anomalies where there are one or more cysts in the kidneys. Polycystic kidney disease is a genetic disease that causes cysts to grow inside the kidneys and the kidneys grow larger than they should. It can also cause cysts to develop in the liver and elsewhere in the body. Cystic kidney disease may cause high blood pressure, blood in urine, kidney infections, kidney stones or kidney failure. Early detection and treatment can reduce or prevent complications.
Exstrophy of urinary bladder
Exstrophy of urinary bladder is an anomaly where the bladder opens into the abdominal wall between the umbilicus and the pubic bone. It is often associated with epispadias and structural anomalies of the pubic bones. Without treatment, babies born with bladder exstrophy will be unable to hold urine. Surgery is undertaken to prevent kidney damage and to correct the functioning and appearance of the urinary system and genitals.
Other urinary system
Other urinary system anomalies include:
Any urinary system
Includes anomalies of the ureters, kidneys and bladder.
Sources: Abeywardana and Sullivan 2008; GARD 2020; ICBDSR 2014; Mayo Clinic 2020; NCBDDD 2020; NHS 2020; NORD 2020; OMIM 2020; Orphanet 2020; RCH 2020; Shaun and Shen 2006; WHO et al. 2014.
The following resources have more detailed clinical information on specific congenital anomalies and rare diseases.
Abeywardana S and Sullivan EA (2008) Congenital anomalies in Australia 2002–2003, Birth anomalies series no. 3 Cat. no. PER 41. Sydney: AIHW National Perinatal Statistics Unit.
GARD (Genetic and Rare Disease Information Center) (2020) Genetic and Rare Diseases Information [website], accessed August 2020.
Human Phenotype Ontology (2021) Human phenotype ontology [website], accessed September 2021.
ICBDSR (International Clearinghouse for Birth Defects Surveillance and Research) (2014) Annual report 2014, ICBDSR [website], accessed, September 2021.
Mayo Clinic (2020) Patient care and health information [website], accessed August 2020.
NCBDDD (National Center on Birth Defects and Developmental Disabilities) (2020) National Center on Birth Defects and Developmental Disabilities, National Center on Birth Defects and Developmental Disabilities Home | NCBDDD | CDC, accessed August 2020.
NHS (National Health Service) (2020) Health A to Z - NHS (www.nhs.uk), accessed August 2020.
NORD (National Organisation of Rare Disorders) (2020) National Organisation of Rare Disorders, Home - NORD (National Organization for Rare Disorders) (rarediseases.org), accessed August 2020.
OMIM Online Mendelian Inheritance in Man (2020) An Online Catalog of Human Genes and Genetic Disorders, OMIM - Online Mendelian Inheritance in Man, accessed August 2020.
Orphanet (2020) The portal for rare diseases and orphan drugs [website], accessed August 2020.
RCH (Royal Children’s Hospital Melbourne) (2020) Kids Health Information, The Royal Children’s Hospital Melbourne website, accessed August 2020.
Shaun PS and Shen I (2006) Atrioventricular Septal Defects in Nichols DG, Underleiger RM, Spevak PJ, Greenly WJ, Cameron, DE, Lappe, DG and Wetzel RC (eds) Critical Heart Disease in Infants and Children, 2nd edn, Philadelphia: Elsevier.
WHO (World Health Organization), National Center on Birth Defects and Developmental Disabilities from the United States Centers for Disease Control and Prevention and International Clearinghouse for Birth Defects Surveillance and Research (2014) Birth defects surveillance atlas of selected congenital anomalies, Geneva: World Health Organization.
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