Twenty to 27% of individuals with a laryngeal cleft also have a tracheoesophageal fistula and approximately 6% of individuals with a fistula also have a cleft. Other congenital anomalies commonly associated with laryngeal cleft are gastro-oesophageal reflux, tracheobronchomalacia, congenital heart defect, dextrocardia and situs inversus. Laryngeal cleft can also be a component of other genetic syndromes, including Pallister-Hall syndrome and G syndrome (Opitz-Friaz syndrome).

Neonates with TEF or esophageal atresia are unable to feed properly. Once diagnosed, prompt surgery is required to allow the food intake. Some children do experience problems following TEF surgery; they can develop dysphagia and thoracic problems. Children with TEF can also be born with other abnormalities, most commonly those described in VACTERL association - a group of anomalies which often occur together, including heart, kidney and limb deformities. 6% of babies with TEF also have a laryngeal cleft.

A laryngeal cleft or laryngotracheoesophageal cleft is a rare congenital abnormality in the posterior laryngo-tracheal wall. It occurs in approximately 1 in 10,000 to 20,000 births. It means there is a communication between the oesophagus and the trachea, which allows food or fluid to pass into the airway.

The incidence of VACTERL association is estimated to be approximately 1 in 10,000 to 1 in 40,000 live-born infants. It is seen more frequently in infants born to diabetic mothers. While most cases are sporadic, there are clearly families who present with multiple involved members.

Patients with abnormal cardiac and kidney function may be more at risk for hemolytic uremic syndrome

Surgical repair can sometimes result in complications, including:

- Stricture, due to gastric acid erosion of the shortened esophagus

- Leak of contents at the point of anastomosis

- Recurrence of fistula

- Gastro-esophageal reflux disease

- Dysphagia

- Asthma-like symptoms, such as persistent coughing/wheezing

- Recurrent chest infections

- Tracheomalacia

Tracheal agenesis is a rare birth defect with a prevalence of less than 1 in 50,000, in which the trachea fails to develop. The defect is normally fatal, although occasional cases have been reported of long-term survival following surgical intervention.

There are three main types of tracheal agenesis, designated Types I, II and III.

In 2013, a case was reported of a South Korean child with tracheal agenesis who had been successfully treated after having been kept alive in an intensive care unit for the first two and a half years of her life. She then had an artificially created trachea implanted that had been created by tissue engineering using her own stem cells. The patient however later died from complications.

It occurs in approximately 1 in 2500 live births.

Congenital esophageal atresia (EA) represents a failure of the esophagus to develop as a continuous passage. Instead, it ends as a blind pouch. Tracheoesophageal fistula (TEF) represents an abnormal opening between the trachea and esophagus. EA and TEF can occur separately or together. EA and TEF are diagnosed in the ICU at birth and treated immediately.

The presence of EA is suspected in an infant with excessive salivation (drooling) and in a newborn with drooling that is frequently accompanied by choking, coughing and sneezing. When fed, these infants swallow normally but begin to cough and struggle as the fluid returns through the nose and mouth. The infant may become cyanotic (turn bluish due to lack of oxygen) and may stop breathing as the overflow of fluid from the blind pouch is aspirated (sucked into) the trachea. The cyanosis is a result of laryngospasm (a protective mechanism that the body has to prevent aspiration into the trachea). Over time respiratory distress will develop.

If any of the above signs/symptoms are noticed, a catheter is gently passed into the esophagus to check for resistance. If resistance is noted, other studies will be done to confirm the diagnosis. A catheter can be inserted and will show up as white on a regular x-ray film to demonstrate the blind pouch ending. Sometimes a small amount of barium (chalk-like liquid) is placed through the mouth to diagnose the problems.

Treatment of EA and TEF is surgery to repair the defect. If EA or TEF is suspected, all oral feedings are stopped and intravenous fluids are started. The infant will be positioned to help drain secretions and decrease the likelihood of aspiration. Babies with EA may sometimes have other problems. Studies will be done to look at the heart, spine and kidneys.

Surgery to repair EA is essential as the baby will not be able to feed and is highly likely to develop pneumonia. Once the baby is in condition for surgery, an incision is made on the side of the chest. The esophagus can usually be sewn together. Following surgery, the baby may be hospitalized for a variable length of time. Care for each infant is individualized.

Its very commonly seen in a newborn with imperforate anus.

A method for repairing long-gap esophageal atresia using magnets has been developed, that does not require replacing the missing section with grafts of the intestine or other body parts. Using electromagnetic force to attract the upper and lower ends of the esophagus together was first tried in the 1970s by using steel pellets attracted to each other by applying external electromagnets to the patient. In the 2000s a further refinement was developed by Mario Zaritzky's group and others. The newer method uses permanent magnets and a balloon.

1. The magnets are inserted into the upper pouch via the baby's mouth or nose, and the lower via the gastrotomy feeding tube hole (which would have had to be made anyway to feed the baby, therefore not requiring any additional surgery).

2. The distance between the magnets is controlled by a balloon in the upper pouch, between the end of the pouch and the magnet. This also controls the force between the magnets so it is not strong enough to cause damage.

3. After the ends of the esophagus have stretched enough to touch, the upper magnet is replaced by one without a balloon and the stronger magnetic attraction causes the ends to fuse (anastomosis).

In April 2015 Annalise Dapo became the first patient in the United States to have their esophageal atresia corrected using magnets.

Atresia is a condition in which an orifice or passage in the body is (usually abnormally) closed or absent.

Examples of atresia include:

- Biliary atresia, a condition in newborns in which the common bile duct between the liver and the small intestine is blocked or absent.

- Choanal atresia, blockage of the back of the nasal passage, usually by abnormal bony or soft tissue.

- Esophageal atresia, which affects the alimentary tract and causes the esophagus to end before connecting normally to the stomach.

- Imperforate anus, malformation of the opening between the rectum and anus.

- Intestinal atresia, malformation of the intestine, usually resulting from a vascular accident in utero.

- Microtia, absence of the ear canal or failure of the canal to be tubular or fully formed (can be related to Microtia, a congenital deformity of the pinna, or outer ear).

- Ovarian follicle atresia, the degeneration and subsequent resorption of one or more immature ovarian follicles.

- Potter sequence, congenital decreased size of the kidney leading to absolutely no functionality of the kidney, usually related to a single kidney.

- Pulmonary atresia, malformation of the pulmonary valve in which the valve orifice fails to develop.

- Renal agenesis, only having one kidney.

- Tricuspid atresia, a form of congenital heart disease whereby there is a complete absence of the tricuspid valve, and consequently an absence of the right atrioventricular connection.

- Vaginal atresia, a congenital occlusion of the vagina or subsequent adhesion of the walls of the vagina, resulting in its occlusion.

Little is known regarding the exact causes of aortic arch anomalies. However, the association with chromosome 22q11 deletion (CATCH 22) implies that a genetic component is likely in certain cases. Esophageal atresia also occurs in some patients with double aortic arch.

Complete vascular rings represent about 0.5-1% of all congenital cardiovascular malformations. The majority of these are double aortic arches.

There is no known gender preference, i.e. males and females are about equally affected. There is also no known ethnic or geographic disposition.

Associated cardiovascular anomalies are found in 10-15% of patients. These include:

- Atrial septal defect (ASD)

- Ventricular septal defect (VSD)

- Patent ductus arteriosus (PDA)

- Tetralogy of Fallot (ToF)

- Transposition of the great arteries (D-TGA)

The condition arises from some factor or set of factors present during approximately the 3rd week to 7th week of fetal development. Formation of the sacrum/lower back and corresponding nervous system is usually nearing completion by the 4th week of development. Due to abnormal gastrulation, the mesoderm migration is disturbed. This disturbance results in symptoms varying from minor lesions of the lower vertebrae to more severe symptoms such as complete fusion of the lower limbs. While the exact cause is unknown, it has been speculated that the condition may be associated with certain dietary deficiencies including a lack or insufficient amounts of folic acid.

Sacral agenesis syndrome (agenesis of the lumbar spine, sacrum, and coccyx, and hypoplasia of the lower extremities) is a well-established congenital anomaly associated with maternal diabetes mellitus (not gestational diabetes). However, other causes are presumably involved, as demonstrated by the rare incidence of caudal regression syndrome (1:60,000) compared to diabetes.

The dominant inherited sacral agenesis (also referred to as Currarino syndrome) is very often correlated with a mutation in the Hb9 (also called HlxB9) gene (shown by Sally Ann Lynch, 1995, Nature Genetics).

It may be the cause of sirenomelia ("Mermaid syndrome").

Caudal regression syndrome or sacral agenesis (or hypoplasia of the sacrum) is a congenital disorder in which there is abnormal fetal development of the lower spine—the caudal partition of the spine.

It occurs at a rate of approximately one per 25,000 live births.

Studies suggest that prenatal care for mothers during their pregnancies can prevent congenital amputation. Knowing environmental and genetic risks is also important. Heavy exposure to chemicals, smoking, alcohol, poor diet, or engaging in any other teratogenic activities while pregnant can increase the risk of having a child born with a congenital amputation. Folic acid is a multivitamin that has been found to reduce birth defects.

Surgical repair is performed. Reconstruction or ligation of aberrant right subclavian artery by sternotomy/by neck approach.

The exact cause of congenital amputation is unknown and can result from a number of causes. However, most cases show that the first three months in a pregnancy are when most birth defects occur because that is when the organs of the fetus are beginning to form. One common cause is amniotic band syndrome, which occurs when the inner fetal membrane (amnion) ruptures without injury to the outer membrane (chorion). Fibrous bands from the ruptured amnion float in the amniotic fluid and can get entangled with the fetus, thus reducing blood supply to the developing limbs to such an extent that the limbs can become strangulated; the tissues die and are absorbed into the amniotic fluid. A baby with congenital amputation can be missing a portion of a limb or the entire limb, which results in the complete absence of a limb beyond a certain point where only a stump is left is known as transverse deficiency or amelia. When a specific part is missing, it is referred to as longitudinal deficiency. Finally, phocomelia occurs when only a mid-portion of a limb is missing; for example when the hands or feet are directly attached to the trunk of the body.

Amnion ruptures can be caused by:

- teratogenic drugs (e.g. thalidomide, which causes phocomelia), or environmental chemicals

- ionizing radiation (atomic weapons, radioiodine, radiation therapy)

- infections

- metabolic imbalance

- trauma

Congenital amputation is the least common reason for amputation, but it is projected that one in 2000 babies are born each year with a missing or deformed limb. During certain periods in history, an increase in congenital amputations has been documented. One example includes the thalidomide tragedy that occurred in the 1960s when pregnant mothers were given a tranquilizer that contained the harmful drug, which produced an increase in children born without limbs. Another example was the 1986 Chernobyl catastrophe in Ukraine, where the radiation exposure caused many children to be born with abnormal or missing limbs .

Opitz G/BBB Syndrome is a rare genetic condition caused by one of two major types of mutations: MID1 mutation on the short (p) arm of the X chromosome or a mutation of the 22q11.2 gene on the 22nd chromosome. Since it is a genetic disease, it is an inherited condition. However, there is an extremely wide variability in how the disease presents itself.

In terms of prevention, several researchers strongly suggest prenatal testing for at-risk pregnancies if a MID1 mutation has been identified in a family member. Doctors can perform a fetal sex test through chromosome analysis and then screen the DNA for any mutations causing the disease. Knowing that a child may be born with Opitz G/BBB syndrome could help physicians prepare for the child’s needs and the family prepare emotionally. Furthermore, genetic counseling for young adults that are affected, are carriers or are at risk of carrying is strongly suggested, as well (Meroni, Opitz G/BBB syndrome, 2012). Current research suggests that the cause is genetic and no known environmental risk factors have been documented. The only education for prevention suggested is genetic testing for at-risk young adults when a mutation is found or suspected in a family member.

During development of aortic arch, if the proximal portion of the right fourth arch disappears instead of distal portion, the right subclavian artery will arise as the last branch of aortic arch. It then courses behind the esophagus (or rarely in front of esophagus, or even in front of trachea) to supply blood to right arm. This causes pressure on esophagus and results in dysphagia. It can sometimes result in upper gastrointestinal tract bleeding.

TIF is a rare condition with a .7% frequency, and an mortality rate approaching 100% without surgical intervention. Immediate diagnosis and intervention of an TIF is critical for the surgical intervention success. 25-30% of TIF patients who reach the operating room survive. Recently, the incidence of TIF may have declined due to advances in tracheostomy tube technology and the introduction of the bedside percutaneous dilatational tracheostomy (PDT).

Courses of treatment typically include the following:

- Draining the pus once awhile as it can build up a strong odor

- Antibiotics when infection occurs.

- Surgical excision is indicated with recurrent fistular infections, preferably after significant healing of the infection. In case of a persistent infection, infection drainage is performed during the excision operation. The operation is generally performed by an appropriately trained specialist surgeon e.g. an otolaryngologist or a specialist General Surgeon.

- The fistula can be excised as a cosmetic operation even though no infection appeared. The procedure is considered an elective operation in the absence of any associated complications.

A vascular ring is a congenital defect in which there is an abnormal formation of the aorta and/or its surrounding blood vessels. The trachea and esophagus are completely encircled and sometimes compressed by a "ring" formed by these vessels, which can lead to breathing and digestive difficulties.

Most often this is because of persistence of the double aortic arch after the second month of fetal life.

Infants with vascular rings typically present before 12 months with respiratory or esophageal symptoms like stridor, wheezing, cough, dysphagia, or difficulty feeding. The stridor improves with neck extension, differentiating from laryngomalacia which is relieved by prone or upright positioning, and will not be relieved with corticosteroids or epinephrine, unlike croup. Diagnosis requires a high degree of clinical suspicion and can be confirmed with barium contrast esophagogram for those with esophageal symptoms, bronchoscopy, or CT or MRI.

Laryngotracheal stenosis (Laryngo-: Glottic Stenosis; Subglottic Stenosis; Tracheal: narrowings at different levels of the windpipe) is a more accurate description for this condition when compared, for example to subglottic stenosis which technically only refers to narrowing just below vocal folds or tracheal stenosis. In babies and young children however, the subglottis is the narrowest part of the airway and most stenoses do in fact occur at this level. Subglottic stenosis is often therefore used to describe central airway narrowing in children, and laryngotracheal stenosis is more often used in adults.

Laryngotracheal stenosis refers to abnormal narrowing of the central air passageways. This can occur at the level of the larynx, trachea, carina or main bronchi.

In a small number of patients narrowing may be present in more than one anatomical location.