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.

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.

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.

Treatment of a laryngeal cleft depends on the length and resulting severity of symptoms. A shallow cleft (Type I) may not require surgical intervention. Symptoms may be able to be managed by thickening the infant's feeds. If symptomatic, Type I clefts can be sutured closed or injected with filler as a temporary fix to determine if obliterating the cleft is beneficial and whether or not a more formal closure is required at a later date. Slightly longer clefts (Type II and short Type III) can be repaired endoscopically. Short type IV clefts extending to within 5 mm below the innominate artery can be repaired through the neck by splitting the trachea vertically in the midline and suturing the back layers of the esophagus and trachea closed. A long, tapered piece of rib graft can be placed between the esophageal and tracheal layers to make them rigid so the patient will not require a tracheotomy after the surgery and to decrease chances of fistula postoperatively. Long Type IV clefts extending further than 5 mm below the innominate artery cannot be reached with a vertical incision in the trachea, and therefore are best repaired through cricotracheal resection. This involves separating the trachea from the cricoid cartilage, leaving the patient intubated through the trachea, suturing each of the esophagus and the back wall of the trachea closed independently, and then reattaching the trachea to the cricoid cartilage. This prevents the need for pulmonary bypass or extracorporeal membrane oxygenation.

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

With a high lesion, many children have problems controlling bowel function and most also become constipated. With a low lesion, children generally have good bowel control, but they may still become constipated.

For children who have a poor outcome for continence and constipation from the initial surgery, further surgery to better establish the angle between the anus and the rectum may improve continence and, for those with a large rectum, surgery to remove that dilated segment may significantly improve the bowel control for the patient. An antegrade enema mechanism can be established by joining the appendix to the skin (Malone stoma); however, establishing more normal anatomy is the priority.

Esophageal diseases can derive from congenital conditions, or they can be acquired later in life.

Many people experience a burning sensation in their chest occasionally, caused by stomach acids refluxing into the esophagus, normally called heartburn. Extended exposure to heartburn may erode the lining of the esophagus, leading potentially to Barrett's esophagus which is associated with an increased risk of adenocarcinoma most commonly found in the distal one-third of the esophagus.

Some people also experience a sensation known as globus esophagus, where it feels as if a ball is lodged in the lower part of the esophagus.

The following are additional diseases and conditions that affect the esophagus:

- Achalasia

- Acute esophageal necrosis

- Barrett's esophagus

- Boerhaave syndrome

- Caustic injury to the esophagus

- Chagas disease

- Diffuse esophageal spasm

- Esophageal atresia and Tracheoesophageal fistula

- Esophageal cancer

- Esophageal dysphagia

- Esophageal varices

- Esophageal web

- Esophagitis

- GERD

- Hiatus hernia

- Jackhammer esophagus (hypercontractile peristalsis)

- Killian–Jamieson diverticulum

- Mallory-Weiss syndrome

- Neurogenic dysphagia

- Nutcracker esophagus

- Schatzki's ring

- Zenker's Diverticulum

Imperforate anus usually requires immediate surgery to open a passage for feces unless a fistula can be relied on until corrective surgery takes place. Depending on the severity of the imperforate, it is treated either with a perineal anoplasty or with a colostomy.

While many surgical techniques to definitively repair anorectal malformations have been described. The posterior sagittal approach (PSARP) has become the most popular. It involves dissection of the perineum without entry into the abdomen and 90% of defects in boys can be repaired this way.

With the exception of a few case reports describing survival without surgery, the mortality of untreated Boerhaave syndrome is nearly 100%. Its treatment includes immediate antibiotic therapy to prevent mediastinitis and sepsis, surgical repair of the perforation, and if there is significant fluid loss it should be replaced with IV fluid therapy since oral rehydration is not possible. Even with early surgical intervention (within 24 hours) the risk of death is 25%.

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.

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).

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.

Temporary alleviation can be achieved by inserting an oral airway into the mouth. However, the only definitive treatment is surgery to correct the defect by perforating the atresia to create a nasopharyngeal airway. If the blockage is caused by bone, this is drilled through and stent inserted. The patient has to have this sucked out by an air vacuum machine . And in later life as a teenager or in early twenties the hole will have to be re-drilled larger.

A stent may be inserted to keep the newly formed airway patent or repeated dilatation may be performed.

With early intervention, morbidity and mortality of cases of intestinal obstruction is low. The outcome is in part dependent upon congenital comorbidities and delays in diagnosis and management.

Duodenal atresia, also known as duodenojejunal atresia, is the congenital absence or complete closure of a portion of the lumen of the duodenum. It causes increased levels of amniotic fluid during pregnancy (polyhydramnios) and intestinal obstruction in newborn babies. Radiography shows a distended stomach and distended duodenum, which are separated by the pyloric valve, a finding described as the double-bubble sign.

Treatment includes suctioning out any fluid that is trapped in the stomach, providing fluids intravenously, and surgical repair of the intestinal closure.

Intestinal atresia is a malformation where there is a narrowing or absence of a portion of the intestine. This defect can either occur in the small or large intestine.

Some causes of bowel obstruction may resolve spontaneously; many require operative treatment. In adults, frequently the surgical intervention and the treatment of the causative lesion are required. In malignant large bowel obstruction, endoscopically placed self-expanding metal stents may be used to temporarily relieve the obstruction as a bridge to surgery, or as palliation. Diagnosis of the type of bowel obstruction is normally conducted through initial plain radiograph of the abdomen, luminal contrast studies, computed tomography scan, or ultrasonography prior to determining the best type of treatment.

Gastric atresia is the complete occlusion of the pyloric outlet of the stomach and is an extremely rare event.

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.

In the management of small bowel obstructions, a commonly quoted surgical aphorism is: "never let the sun rise or set on small-bowel obstruction" because about 5.5% of small bowel obstructions are ultimately fatal if treatment is delayed. However improvements in radiological imaging of small bowel obstructions allow for confident distinction between simple obstructions, that can be treated conservatively, and obstructions that are surgical emergencies (volvulus, closed-loop obstructions, ischemic bowel, incarcerated hernias, etc.).

A small flexible tube (nasogastric tube) may be inserted through the nose into the stomach to help decompress the dilated bowel. This tube is uncomfortable but does relieve the abdominal cramps, distention, and vomiting. Intravenous therapy is utilized and the urine output is monitored with a catheter in the bladder.

Most people with SBO are initially managed conservatively because in many cases, the bowel will open up. Some adhesions loosen up and the obstruction resolves. However, when conservative management is undertaken, the patient is examined several times a day, and X-ray images are obtained to ensure that the individual is not getting clinically worse.

Conservative treatment involves insertion of a nasogastric tube, correction of dehydration and electrolyte abnormalities. Opioid pain relievers may be used for patients with severe pain. Antiemetics may be administered if the patient is vomiting. Adhesive obstructions often settle without surgery. If the obstruction is complete a surgery is usually required.

Most patients do improve with conservative care in 2–5 days. However, on some occasions, the cause of obstruction may be a cancer and in such cases, surgery is the only treatment. These individuals undergo surgery where the cause of SBO is removed. Individuals who have bowel resection or lysis of adhesions usually stay in the hospital a few more days until they are able to eat and walk.

Small bowel obstruction caused by Crohn's disease, peritoneal carcinomatosis, sclerosing peritonitis, radiation enteritis, and postpartum bowel obstruction are typically treated conservatively, i.e. without surgery.

Neonatal bowel obstruction (NBO) or neonatal intestinal obstruction is the most common surgical emergency in the neonatal period. It may occur due to a variety of conditions and has an excellent outcome based on timely diagnosis and appropriate intervention.

No cure for the condition as such exists. A number of treatments may provide partial relief:

- Botox injections may temporarily disable the muscle and provide relief for 3-4 months per injection

- Muscle relaxants

- Lorazepam (Ativan), diazepam (Valium) and other benzodiazepines relax the smooth muscle in the throat, slowing or halting contractions. In some people, benzodiazepines may have addictive properties.

- Stress reduction

- High stress levels make these spasms more noticeable

- It is advisable to take note of when your symptoms are at their worst

- Warm fluids

- Hot fluids may be helpful for some people with cricopharyngeal spasm (or other esophageal disorders)

Biliary atresia seems to affect females slightly more often than males, and Asians and African Americans more often than Caucasians. It is common for only one child in a pair of twins or within the same family to have the condition. There seems to be no link to medications or immunizations given immediately before or during pregnancy. Diabetes during pregnancy particularly during the first trimester seems to predispose to a number of distinct congenital abnormalities in the infant such as sacral agenesis and the syndromic form of biliary atresia.

Most (>95%) infants with biliary atresia will undergo an operation designed to retain and salvage the native liver, restore bile flow and reduce the level of jaundice. This is known as the Kasai procedure (after Morio Kasai, the Japanese surgeon who first developed the technique) or hepatoportoenterostomy. Although the procedure is not thought of as curative, it may relieve jaundice, and stop liver fibrosis allowing normal growth and development. Published series from Japan, North America and the UK show that bilirubin levels will fall to normal values in about 50-55% of infants allowing 40-50% to retain their own liver to reach the age of 5 and 10 years (and beyond). Liver transplantation is an option for those children whose liver function and symptoms fail to respond to a Kasai operation.

Recent large-scale studies by Davenport et al. ("Annals of Surgery", 2008) show that the age of the patient is not an absolute clinical factor affecting prognosis. The influence of age differs according to the disease etiology—i.e., whether biliary atresia is isolated, cystic (CBA), or accompanied by splenic malformation (BASM).

It is widely accepted that corticosteroid treatment after a Kasai operation, with or without choleretics and antibiotics, has a beneficial effect on postoperative bile flow and can clear jaundice, but the dosing and duration of the ideal steroid protocol are controversial. Furthermore, it has been observed in many retrospective longitudinal studies that corticosteroid treatment does not prolong survival of the native liver or transplant-free survival. Davenport et al. also showed ("Hepatology" 2007) that short-term, low-dose steroid therapy following a Kasai operation had no effect on the mid- or long-term prognosis of biliary atresia patients.