Fetal and neonatal intestinal atresia are treated using laparotomy after birth. If the area affected is small, the surgeon may be able to remove the damaged portion and join the intestine back together. In instances where the narrowing is longer, or the area is damaged and cannot be used for period of time, a temporary stoma may be placed.

The treatment of pentalogy of Cantrell is directed toward the specific symptoms that are apparent in each individual. Surgical intervention for cardiac, diaphragmatic and other associated defects is necessary. Affected infants will require complex medical care and may require surgical intervention. In most cases, pentalogy of Cantrell is fatal without surgical intervention. However, in some cases, the defects are so severe that the individual dies regardless of the medical or surgical interventions received.

The specific treatment strategy will vary from one infant to another based upon various factors, including the size and type of abdominal wall defect, the specific cardiac anomalies that are present, and the particular type of ectopia cordis. Surgical procedures that may be required shortly after birth include repair of an omphalocele. At this time, physicians may also attempt to repair certain other defects including defects of the sternum, diaphragm and the pericardium.

In severe cases, some physicians advocate for a staged repair of the defects associated with pentalogy of Cantrell. The initial operation immediately after birth provides separation of the peritoneal and pericardial cavities, coverage of the midline defect and repair of the omphalocele. After appropriate growth of the thoracic cavity and lungs, the second stage consists of the repair of cardiac defects and return of the heart to the chest. Eventually, usually by age 2 or 3, reconstruction of the lower sternum or epigastrium may be necessary.

Other treatment of pentalogy of Cantrell is symptomatic and supportive.

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.

Early treatment includes removing fluids from the stomach via a nasogastric tube, and providing fluids intravenously. The definitive treatment for duodenal atresia is surgery (duodenoduodenostomy), which may be performed openly or laparoscopically. The surgery is not urgent. The initial repair has a 5 percent morbidity and mortality rate.

Treatments for the condition vary depending on its severity. The most immediate and effective treatment in the majority of cases is a surgical repair to close the fistula/s and reconnect the two ends of the esophagus to each other. Although this is usually done through an incision between the ribs on right side of the baby, a technique using three small incisions (thoracoscopy) is being used at some centers. In a minority of cases, the gap between upper and lower esophageal segments may be too long to bridge. In some of these so-called long gap cases, though, an advanced surgical treatment developed by John Foker, MD, may be utilized to elongate and then join together the short esophageal segments. Using the Foker technique, surgeons place traction sutures in the tiny esophageal ends and increase the tension on these sutures daily until the ends are close enough to be sewn together. The result is a normally functioning esophagus, virtually indistinguishable from one congenitally well formed. Unfortunately, the results have been somewhat difficult to replicate by other surgeons and the need for multiple operations has tempered enthusiasm for this approach.

The optimal treatment in cases of long gap esophageal atresia remains controversial. Traditional surgical approaches include gastrostomy followed by gastric pull-up, colonic transposition and jejunum transposition. Gastric pull-up has been the preferred approach at many specialized centers, including Great Ormond Street (London) and Mott Children's Hospital (Ann Arbor). Gastrostomy, or G-tube, allows for tube feedings into the stomach through the abdominal wall. Often a cervical esophagostomy will also be done, to allow the saliva which is swallowed to drain out a hole in the neck. Months or years later, the esophagus may be repaired, sometimes by using a segment of bowel brought up into the chest, interposing between the upper and lower segments of esophagus.

Post operative complications sometimes arise, including a leak at the site of closure of the esophagus. Sometimes a stricture, or tight spot, will develop in the esophagus, making it difficult to swallow. This can usually be dilated using medical instruments. In later life, most children with this disorder will have some trouble with either swallowing or heartburn or both. Esophageal dismotility occurs in 75-100% of patients.

Tracheomalacia—a softening of the trachea, usually above the carina (carina of trachea), but sometimes extensive in the lower bronchial tree as well—is another possible serious complication. Even after esophageal repair (anastomosis) the relative flaccidity of former proximal pouch (blind pouch, above) along with esophageal dysmotility can cause fluid buildup during feeding. Owing to proximity, pouch ballooning can cause tracheal occlusion. Severe hypoxia ("dying spells") follows and medical intervention can often be required.

A variety of treatments for tracheomalacia associated with esophageal atresia are available. If not severe, the condition can be managed expectantly since the trachea will usually stiffen as the infant matures into the first year of life. When only the trachea above the carina is compromised, one of the "simplest" interventions is aortopexy wherein the aortic loop is attached to the rear of the sternum, thereby mechanically relieving pressure from the softened trachea. An even simpler intervention is stenting. However, epithelial cell proliferation and potential incorporation of the stent into the trachea can make subsequent removal dangerous.

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.

The occurrence of ectopia cordis is 8 per million births. It is typically classified according to location of the ectopic heart, which includes:

- Cervical

- Thoracic

- Thoracoabdominal

- Abdominal

Thoracic and thoraco-abdominal ectopia cordis constitute the vast majority of known cases.

The condition was initially thought untreatable until surgeon Alfred Blalock, cardiologist Helen B. Taussig, and lab assistant Vivien Thomas at Johns Hopkins University developed a palliative surgical procedure, which involved forming a side to end anastomosis between the subclavian artery and the pulmonary artery. This first surgery was depicted in the film "Something the Lord Made". It was actually Helen Taussig who convinced Alfred Blalock that the shunt was going to work. This redirected a large portion of the partially oxygenated blood leaving the heart for the body into the lungs, increasing flow through the pulmonary circuit, and greatly relieving symptoms in patients. The first Blalock-Thomas-Taussig shunt surgery was performed on 15-month-old Eileen Saxon on November 29, 1944 with dramatic results.

The Potts shunt and the Waterston-Cooley shunt are other shunt procedures which were developed for the same purpose. These are no longer used.

Currently, Blalock-Thomas-Taussig shunts are not normally performed on infants with TOF except for severe variants such as TOF with pulmonary atresia (pseudotruncus arteriosus).

Due to the rarity and rapid postpartum mortality of ectopia cordis, limited treatment options have been developed. Only one successful surgery has been performed as of now, and the mortality rate remains high.

The most common cause of non-duodenal intestinal atresia is a vascular accident in utero that leads to decreased intestinal perfusion and ischemia of the respective segment of bowel. This leads to narrowing, or in the most severe cases, complete obliteration of the intestinal lumen.

In the case that the superior mesenteric artery, or another major intestinal artery, is occluded, large segments of bowel can be entirely underdeveloped. Classically, the affected area of bowel assumes a spiral configuration and is described to have an "apple peel" like appearance; this is accompanied by lack of a dorsal mesentery.

Ileal atresia can also result as a complication of meconium ileus.

Tetralogy of Fallot occurs approximately 400 times per million live births and accounts for 7 to 10% of all congenital heart abnormalities.

It is surgically corrected, with resection of any fistula and anastomosis of any discontinuous segments.

The prognosis for pulmonary atresia varies for every child, if the condition is left uncorrected it may be fatal, but the prognosis has greatly improved over the years for those with pulmonary atresia. Some factors that affect how well the child does include how well the heart is beating, and the condition of the blood vessels that supply the heart. Most cases of pulmonary atresia can be helped with surgery, if the patient's right ventricle is exceptionally small, many surgeries will be needed in order to help stimulate normal circulation of blood to the heart.If uncorrected, babies with this type of congenital heart disease may only survive for the first few days of life. Many children with pulmonary atresia will go on to lead normal lives, though complications such as endocarditis, stroke and seizures are possible.

Each of the symptoms of situs ambiguous must be managed with appropriate treatment dependent upon the organ system involved. Intestinal malrotation is treated surgically using the Ladd procedure. This procedure widens a fold in the peritoneum so that the intestines can be placed in non-rotated formation. Unfortunately, it is not possible to return the bowel to a normal morphology However, 89% of patients that undergo the Ladd surgery experience a complete resolution of symptoms.

Following cholangiogram, a Kasai Procedure is usually performed in cases of biliary atresia. In this surgery, a Y-shaped shunt is used to passage bile from the liver directly to the intestine. If this is unsuccessful, liver transplantation can be considered based on the overall health of the patient. Fortunately, the Kasai Procedure is successful in approximately 80% of patients. Following the operation, patients are advised to take fat-soluble vitamins, choleretics, and anti-inflammatory medications.

Functionally asplenic patients have an elevated lifetime risk of septicemia, as they have no functional spleen for fighting infection. For this reason, asplenic patients are under constant observation for any signs of fever or infection. In the case of infection, patients are placed on controlled empiric antibiotic therapy to avoid development of antibiotic resistance. This therapy battles infection by both gram-positive and gram-negative bacteria.

Right-atrial and left-atrial isomerism and associated pulmonary issues are treated in a series of steps based on the severity of symptoms. Isomeric patients are first treated by inserting a shunt that will move incoming blood through the pulmonary circuit. The Fontan procedure routes blood through the patient's single ventricle, to the lungs, and into systemic circulation. This process is favorable in patients aged 2 – 5 years old. Unfortunately, 20-30% of patients will require a heart transplant. Left-atrial isomeric patients have less severe complications, as they typically have 2 functional ventricles. In this case, they can undergo biventricular repair to form 2 separate ventricles and functional associated valves.

Prognosis for patients with situs ambiguous is quite varied, considering the spectrum of clinical complications. Infants who experience severe cyanosis at birth die within hours of delivery if medical intervention is not immediate. Alternatively, longevity of neonates with mild cardiac lesions is unaffected. Ten percent of patients born with right atrial isomerism die by the age of 5 without intervention. Fortunately, improvements in therapies has increased the 5-year survival to 30-74% for right atrial isomeric patients and 65-84% for left atrial isomeric patients based on the cause of their disease.

In terms of the cause of pulmonary atresia, there is uncertainty as to what instigates this congenital heart defect. Potential risk factors that can cause this congenital heart defect are those the pregnant mother may come in contact with, such as:

- Certain medications

- Diet

- Smoking

Although its cause is poorly understood, situs ambiguous has been linked to family history of malformations and maternal cocaine use, suggesting both genetic and environmental factors play a role. Several genes in the TGF-beta pathway, which controls left-right patterning of viseral organs across the body axis, have been indicated in sporadic and familial cases of atrial isomerism.

There does not appear to be a screening method for prevention of heterotaxy syndrome. However, genetic testing in family members that display atrial isomerism or other cardiac malformations may help to discern risk for additional family members, especially in X-linked causes of heterotaxy syndrome.

Sometimes CHD improves without treatment. Other defects are so small that they do not require any treatment. Most of the time CHD is serious and requires surgery and/or medications. Medications include diuretics, which aid the body in eliminating water, salts, and digoxin for strengthening the contraction of the heart. This slows the heartbeat and removes some fluid from tissues. Some defects require surgical procedures to restore circulation back to normal and in some cases, multiple surgeries are needed.

Interventional cardiology now offers patients minimally invasive alternatives to surgery for some patients. The Melody Transcatheter Pulmonary Valve (TPV), approved in Europe in 2006 and in the U.S. in 2010 under a Humanitarian Device Exemption (HDE), is designed to treat congenital heart disease patients with a dysfunctional conduit in their right ventricular outflow tract (RVOT). The RVOT is the connection between the heart and lungs; once blood reaches the lungs, it is enriched with oxygen before being pumped to the rest of the body. Transcatheter pulmonary valve technology provides a less-invasive means to extend the life of a failed RVOT conduit and is designed to allow physicians to deliver a replacement pulmonary valve via a catheter through the patient’s blood vessels.

Most patients require lifelong specialized cardiac care, first with a pediatric cardiologist and later with an adult congenital cardiologist. There are more than 1.8 million adults living with congenital heart defects.

Surgical correction is indicated in all double aortic arch patients with obstructive symptoms (stridor, wheezing, pulmonary infections, poor feeding with choking). If symptoms are absent a conservative approach (watchful waiting) can be reasonable. Children with very mild symptoms may outgrow their symptoms but need regular follow-up.

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.

After the surgery, some patients require intubation and mechanical ventilation for several days to allow adequate tracheal toilet, but most patients can have the tubes removed soon after the surgery. The obstructive airway symptoms may be worse in the first postoperative weeks. Only a few patients have immediate relief of stridor, but many obtain immediate relief of problems with swallowing (dysphagia). After extubation, it might be necessary to maintain positive airway pressure by appropriate flows of a humidified oxygen/air mixture.

Pentalogy of Cantrell (or thoraco-abdominal syndrome) is a rare syndrome that causes defects involving the diaphragm, abdominal wall, pericardium, heart and lower sternum.

Its prevalence is less than 1 in 1000000.

It was characterized in 1958.

A locus at Xq25-26 has been described.

When there are holes in the septum that divide the four chambers of the heart the oxygen-rich blood and oxygen-poor blood mix this creates more stress on the heart to pump blood to where oxygen is needed. As a result, you get enlargement of the heart, heart failure (being unable to adequately supply body with needed oxygen, pulmonary hypertension, and pneumonia.

The development of pulmonary hypertension is very serious. And this because the left ventricle is weakened due to its overuse. When this happens, the pressure backs up into the pulmonary veins and the lungs. This type of damage is irreversible which is why immediate treatment is recommended after diagnosis.

Very few risk factors for choanal atresia have been identified. While causes are unknown, both genetic and environmental triggers are suspected. One study suggests that chemicals that act as endocrine disrupters may put an unborn infant at risk. A 2012 epidemiological study looked at atrazine, a commonly used herbicide in the U.S., and found that women who lived in counties in Texas with the highest levels of this chemical being used to treat agricultural crops were 80 times more likely to give birth to infants with choanal atresia or stenosis compared to women who lived in the counties with the lowest levels. Another epidemiological report in 2010 found even higher associations between increased incidents of choanal atresia and exposure to second-hand-smoke, coffee consumption, high maternal zinc and B-12 intake and exposure to anti-infective urinary tract medications.

In the movie City of Angels, Dr. Maggie Rice (played by Meg Ryan) correctly diagnoses the cause of a newborn baby's failure to thrive as due to choanal atresia.

Treatment is surgical and involves closure of the atrial and ventricular septal defects and restoration of a competent left AV valve as far as is possible. Open surgical procedures require a heart-lung machine and are done with a median sternotomy. Surgical mortality for uncomplicated ostium primum defects in experienced centers is 2%; for uncomplicated cases of complete atrioventricular canal, 4% or less. Certain complications such as tetralogy of Fallot or highly unbalanced flow across the common AV valve can increase risk significantly.

Infants born with AVSD are generally in sufficient health to not require immediate corrective surgery. If surgery is not required immediately after birth, the newborn will be closely monitored for the next several months, and the operation held-off until the first signs of lung distress or heart failure. This gives the infant time to grow, increasing the size of, and thereby the ease of operation on, the heart, as well as the ease of recovery. Infants will generally require surgery within three to six months, however, they may be able to go up to two years before the operation becomes necessary, depending on the severity of the defect.