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.

If left untreated, gastroschisis is fatal to the infant; however, in adequate settings the survival rate for treated infants is 90%.

Most risks of gastroschisis are related to decreased bowel function. Sometimes blood flow to the exposed organs is impaired or there may be less than the normal amount of intestine. This may put infants at risk for other dangerous conditions such as necrotizing enterocolitis. Also, because their intestines are exposed, infants with gastroschisis are at increased risk for infection, and must be closely monitored.

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.

Gastroschisis requires surgical treatment to return the exposed intestines to the abdominal cavity and close the hole in the abdomen. Sometimes this is done immediately but more often the exposed organs are covered with sterile drapings, and only later is the surgery done. Affected newborns frequently require more than one surgery, as only about 10% of cases can be closed in a single surgery.

Given the urgent need for surgery after birth, it is recommended that delivery occur at a facility equipped for caring for these high-risk neonates, as transfers to other facilities may increase risk of adverse outcomes. There is no evidence that cesarean deliveries lead to better outcomes for babies with gastroschisis, so cesarean delivery is only considered if there are other indications.

The main cause for lengthy recovery periods is the time taken for the infant's bowel function to return to normal. After surgery infants are fed through IV fluids and gradually introduced to normal feeding.

In France, Aymé, "et al." (1989) estimated the prevalence of Fryns syndrome to be 0.7 per 10,000 births based on the diagnosis of 6 cases in a series of 112,276 consecutive births (live births and perinatal deaths).

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.

A famous case of IND is that of Adele Chapman, who had a triple transplant of the small intestine, pancreas and liver, the first of its kind in the UK; therefore the official charity of IND is the Adele Chapman Foundation.

Conservative treatment involves the long term use of laxatives and enemas, and has limited success. Dietary changes in order to control the disease are ineffective and high fiber diets often worsen the symptoms in children. As a last resort, surgical treatment (internal sphincter myectomy or colon resection) is used. In extreme cases, the only effective cure is a complete transplant of the affected parts.

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.

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

In order to treat a Bochdalek hernia, the baby's physician must take into account multiple factors. First, the diagnosis will vary depending on whether the Bochdalek hernia was found during fetal development or after birth. "The key to survival lies in prompt diagnosis and treatment." Second, the baby's overall health and medical history will be evaluated. Third, the doctor will look at the seriousness of the condition. Fourth, the baby will need to be evaluated at the level of medication, procedure and therapy he or she can handle, and finally, the doctor will take into consideration the opinion and preference of the parents. After these things are all taken into consideration and evaluated, the doctor will determine how to treat the baby. There are three different treatments available. The first treatment includes the baby's admission into the NICU (Neonatal Intensive Care Unit). In most Bochdalek Hernia cases, babies who are admitted in the NICU, are placed on a mechanical ventilator to help breathing. Another treatment involves putting the infants on a temporary heart/lung bypass machine, called an ECMO. This normally pertains to children who have severe problems. ECMO performs the tasks the regularly functioning hearts and lungs do. ECMO allows oxygen to be regulated into the blood and then pumps the blood throughout the entire body. Normally, this machine is used to stabilize the baby's condition. The third option in treatment is surgery.

After the baby is stable and his or her state has improved, the diaphragm can be fixed and the misplaced organs can be relocated to their correct position. Although these are various treatments for Bochdalek Hernias, it does not guarantee the baby will survive. Since the baby must go through some or all of the previous treatments, the baby's hospital stay is usually longer than that of a "normal" newborn. The average infants born with a Bochdalek Hernia stay in the hospital between 23.1 and 26.8 days.

Bochdalek hernias make up about 0.17% to 6% of all diaphragmatic hernia cases and about one in every 2200 to 12,500 births every year. Babies who are born with a Bochdalek hernia are more than likely to have another birth defect caused by the hernia. About twenty percent of those children born with a Bochdalek hernia, also have a congenital heart defect. In addition, infants born with this condition may also have other abnormalities. "Between five and sixteen [percent of infants] have a chromosomal abnormality." In most cases, left-sided hernias or Bochdalek hernias have a ratio of 3:2 of males to females. In other words, Bochdalek hernias are more common in men.

The type of treatment, like that of most disorders, depends on the severity of the symptoms. One option is to perform a "vesicostomy", which allows the bladder to drain through a small hole in the abdomen, thus helping to prevent urinary tract infections. Similarly, consistent self catheterization, often several times per day, can be an effective approach to preventing infections. A more drastic procedure is a surgical "remodeling" of the abdominal wall and urinary tract. Boys often need to undergo an orchiopexy, to move the testes to their proper place in the scrotum.

If there are no other defects, the prognosis after surgical repair of this condition is relatively good. However, 10% of those with more severe or additional abnormalities die from it. The organs themselves are fully functional; the difficulty lies in fitting them inside the abdomen. The condition is, in fact, a hernia requiring only replacement and strengthening of the passageway through which it occurred. After surgery, increased pressure in the stretched abdomen can compromise the function of the organs inside.

Abdominal wall defects can be treated surgically if there is no accompanying anomalies. The surgical procedure also called omphalocele repair/closure or gastroschisis repair/closure is not overcomplicated. The organs are normal but are misplaced.

However, if the abdominal cavity is too small or when the organs are too large or swollen to close the skin, it may be difficult to fit all the viscera into the small abdominal cavity. In such cases, the surgeon will place a covering pouch generally made of silastic, commonly called a "silo" (because it's shaped like an agricultural silo), over the abdominal organs on the outside of the infant. The silo serves to conserve heat and prevent infection. The silo is spring-loaded so that the device can be attached to the inside of the abdominal wall without sutures. The top of the silo is secured in a way that causes it to stand upright, so that the bowels are gradually coaxed into the abdominal cavity by gravity. This process can take up to a week, and final closure may be performed a few weeks later. More surgery may be required to repair the abdominal muscles at a later time.

The Swedish-American surgeon, Orvar Swenson (1909–2012), who discovered the cause of Hirschsprung’s, first performed its surgical treatment, the pull-through surgery, in 1948. The pull-through procedure repairs the colon by connecting the functioning portion of the bowel to the anus. The pull-through procedure is the typical method for treating Hirschsprung’s in younger patients. Swenson devised the original procedure, and the pull-through surgery has been modified many times.

Currently, several different surgical approaches are used, which include the Swenson, Soave, Duhamel, and Boley procedures. The Swenson procedure leaves a small portion of the diseased bowel. The Soave procedure, named after the Italian pediatric surgeon, Franco Soave (1917–1984), leaves the outer wall of the colon unaltered. The Boley procedure, pioneered by the American surgeon, Scott Boley (b. 1941), is a small modification of the Soave procedure, so the term "Soave-Boley" procedure is sometimes used. The Duhamel procedure, named for the French pediatric surgeon, Bernard Duhamel (1917–1996), uses a surgical stapler to connect the good and bad bowel.

For the 15% of children who do not obtain full bowel control, other treatments are available. Constipation may be remedied by laxatives or a high-fiber diet. In those patients, serious dehydration can play a major factor in their lifestyles. A lack of bowel control may be addressed by a stoma, similar to a colostomy. The Malone antegrade colonic enema (ACE) is also an option. In a Malone ACE, a tube goes through the abdominal wall to the appendix, or if available, to the colon. The bowel is then flushed daily. Children as young as 6 years of age may administer this daily flush on their own.

If the affected portion of the lower intestine is restricted to the lower portion of the rectum, other surgical procedures may be performed, such as a posterior rectal myectomy.

The prognosis is good in 70% of cases. Chronic postoperative constipation is present in 7 to 8% of the operated cases. Postoperative enterocolitis, a severe manifestation, is present in the 10–20% of operated patients.

Treatment of Hirschsprung's disease consists of surgical removal (resection) of the abnormal section of the colon, followed by reanastomosis.

Current research is focusing on clearly defining the phenotype associated with tetrasomy 18p and identifying which genes cause medical and developmental problems when present in four copies.

Omphalocele, also spelled omphalocoele, is a rare abdominal wall defect in which the intestines, liver, and occasionally other organs remain outside of the abdomen in a sac because of failure of normal return of intestines and other contents back to abdominal cavity during around ninth week of intrauterine development.

Omphalocele occurs in 1/4,000 births and is associated with a high rate of mortality (25%) and severe malformations, such as cardiac anomalies (50%), neural tube defect(40%), exstrophy of bladder and Beckwith Wiedemann syndrome. Approximately 15% of live-born infants with omphalocele have chromosomal abnormalities. About 30% of infants with an omphalocele have other congenital abnormalities.

Treatment is possible and these are the steps taken:

Resuscitate the patient with fluids to stabilize them before surgically

- correcting the malrotation (counterclockwise rotation of the bowel),

- cutting the fibrous bands over the duodenum,

- widening the mesenteric pedicle by separation of the duodenum and cecum.

With this condition the appendix is often on the wrong side of the body and therefore removed as a precautionary measure during the surgical procedure.

One surgical technique is known as "Ladd's procedure", after Dr. William Ladd. Long term research on the Ladd procedure shows that even after the procedure, patients are susceptible to have complaints and might need further surgery.

In a newborn boy thought to have Fryns syndrome, Clark and Fenner-Gonzales (1989) found mosaicism for a tandem duplication of 1q24-q31.2. They suggested that the gene for this disorder is located in that region. However, de Jong et al. (1989), Krassikoff and Sekhon (1990), and Dean et al. (1991) found possible Fryns syndrome associated with anomalies of chromosome 15, chromosome 6, chromosome 8(human)and chromosome 22, respectively. Thus, these cases may all represent mimics of the mendelian syndrome and have no significance as to the location of the gene for the recessive disorder.

By array CGH, Slavotinek et al. (2005) screened patients with DIH and additional phenotypic anomalies consistent with Fryns syndrome for cryptic chromosomal aberrations. They identified submicroscopic chromosome deletions in 3 probands who had previously been diagnosed with Fryns syndrome and had normal karyotyping with G-banded chromosome analysis. Two female infants were found to have microdeletions involving 15q26.2 (see 142340), and 1 male infant had a deletion in band 8p23.1 (see 222400).

Gastroschisis is a similar birth defect, but in gastroschisis the umbilical cord is not involved and the lesion is usually to the right of midline. Parts of organs may be free in the amniotic fluid, and not enclosed in a membranous (peritoneal) sac. Gastroschisis is less frequently associated with other defects than omphalocele.

Omphaloceles occurs more frequently with increased maternal age.

Other related syndromes are Pentalogy of Cantrell, Beckwith-Wiedemann, and OEIS complex (omphalocele, exstrophy of the cloaca, imperforate anus, spinal defects).

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.

Tetrasomy 18p is a genetic condition that is caused by the presence of an isochromosome, composed of two copies of the short arm of chromosome 18. It is characterized by multiple medical and developmental concerns.