The first step in management is orogastric tube placement and securing the airway (intubation). The baby will usually be immediately placed on a ventilator.

Extracorporeal membrane oxygenation (ECMO) has been used as part of the treatment strategy at some hospitals. ECMO acts as a baby heart-lung bypass (though it can be used for older children as well). A venous cannula is inserted into the jugular vein or the common femoral vein(ECMO is divided into two types; (arteriovenous AV and venovenous VV), allowing the blood to exit the body and begin its trek through the ECMO circuit, it is then scrubbed, oxygenated, and passes through a filter before being returned to the body via a second cannula into the baby’s own circulatory system where it makes its rounds before returning to the ECMO circuit to be oxygenated again. In essence, the ECMO circuit acts as the baby's lungs. Babies require extra blood volume and hefty doses of blood thinners in order to keep the circuit running without clot formation, which could be potentially fatal. Even though the baby is not using her lungs, an ocillating ventilator maybe still be used to keep some air in the lungs so that they do not fully collapse while not being used. During ECMO the pulmonary artery has a chance to rest, as it were, thus hopefully reducing the presence of pulmonary hypertension, one of the biggest complication of CDH cases. CDH repair can be done while the baby is on ECMO, although blood thinners increase the risk of bleeding complications. Usually surgeons prefer to perform CDH repairs off ECMO. Once the baby is taken off ECMO the carotid artery is sealed and can no longer be used. When repairing the hernia an incision is made in the abdomen. The hernia can sometimes be simply stitched closed but in more complicated cases a patch may be required. A synthetic patch can be used but will usually require replacement later as the child grows. A more natural patch can be created by slicing and folding over a section of abdominal muscle and securing it to the existing piece of diaphragm. Any organ displacement is corrected during surgery. Though the heart and lungs will usually move back into position on their own, once displaced organs such as bowel, liver, or stomach, are out of the way. The incision is then closed. Sometimes, the incision site will be left open to allow the body to adjust to newly moved organs and the pressure associated with that, and then closed later once swelling and drainage has decreased.

Diaphragm eventration is typically repaired thoracoscopically, by a technique called plication of the diaphragm. Plication basically involves a folding of the eventrated diaphragm which is then sutured in order to “take up the slack” of the excess diaphragm tissue.

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 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.

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.

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.

Surgery is recommended for some types of hernias to prevent complications like obstruction of the bowel or strangulation of the tissue, although umbilical hernias and hiatus hernias may be watched, or are treated with medication. Most abdominal hernias can be surgically repaired, but surgery has complications. Time needed for recovery after treatment is reduced if hernias are operated on laparoscopically. However, open surgery can be done sometimes without general anesthesia. Uncomplicated hernias are principally repaired by pushing back, or "reducing", the herniated tissue, and then mending the weakness in muscle tissue (an operation called herniorrhaphy). If complications have occurred, the surgeon will check the viability of the herniated organ and remove part of it if necessary.

Muscle reinforcement techniques often involve synthetic materials (a mesh prosthesis). The mesh is placed either over the defect (anterior repair) or under the defect (posterior repair). At times staples are used to keep the mesh in place. These mesh repair methods are often called "tension free" repairs because, unlike some suture methods (e.g., Shouldice), muscle is not pulled together under tension. However, this widely used terminology is misleading, as there are many tension-free suture methods that do not use mesh (e.g., Desarda, Guarnieri, Lipton-Estrin, etc.).

Evidence suggests that tension-free methods (with or without mesh) often have lower percentage of recurrences and the fastest recovery period compared to tension suture methods. However, among other possible complications, prosthetic mesh usage seems to have a higher incidence of chronic pain and, sometimes, infection.

The frequency of surgical correction ranges from 10 per 100,000 (U.K.) to 28 per 100,000 (U.S.).

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.

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.

The benefits of the use of an external device to maintain reduction of the hernia without repairing the underlying defect (such as hernia trusses, trunks, belts, etc.) are unclear.

Congenital diaphragmatic hernia has a mortality rate of 40–62%, with outcomes being more favorable in the absence of other congenital abnormalities. Individual rates vary greatly dependent upon multiple factors: size of hernia, organs involved, additional birth defects, and/or genetic problems, amount of lung growth, age and size at birth, type of treatments, timing of treatments, complications (such as infections) and lack of lung function.

Head circumference measurements should be obtained regularly and monitored carefully to detect hydrocephalus. Neurosurgical procedures to relieve hydrocephalus are important. A ventriculoperitoneal shunt may be required in some infants. A pediatric cardiologist should be consulted to manage high-output failure, if present. Often patients need to be intubated. In most cases, the fistulous arteries feeding into the Vein of Galen must be blocked, thereby reducing the blood flow into the vein. Open surgery has a high morbidity and mortality. Recent advances over the past few decades have made endovascular embolization the preferred method of treatment. These treatments are preferred because they offer little threat to the surrounding brain tissue. However, there have been several reported cases of arteriovenous malformations recurring. The young age of many patients, the complex vascular anatomy, and the sensitive location of the Vein of Galen offer considerable challenges to surgeons. Another treatment option is Radiotherapy. Radiotherapy, also called radiosurgery, involves the use of focused beams to damage the blood vessel. Radiotherapy is often not pursued as a treatment because the effects of the procedure can take months or years and there is risk of damaging adjacent brain tissue.

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.

Bochdalek hernia can be a life-threatening condition. Approximately 85.3% of newborns born with a Bochdalek hernia are immediately high risk. Infants born with a Bochdalek hernia have a "high mortality rate due to respiratory insufficiency". Between 25–60% of infants with a Bochdalek hernia die. The lungs, diaphragm, and digestive system are all forming at the same time, so when a Bochdalek hernia permits the abdominal organs to invade the chest cavity rather than remain under the diaphragm in the correct position, it puts the infant in critical condition. These "foreign bodies" in the chest cavity compress the lungs, impairing their proper development and causing pulmonary hypoplasia. Since the lungs of infants suffering from a Bochdalek hernia have fewer alveoli than normal lungs, Bochdalek hernias are life-threatening conditions due to respiratory distress. Also, if the invasion of the intestine or stomach punctures the lung, then the lungs cannot fill completely with air. The baby will not be healthy or stable with this condition because he or she cannot take in enough air and oxygen to keep the body operating properly. Like the lungs, the intestines may also have trouble developing correctly. If the intestines are trapped within the lungs, then the lungs and intestines may not be receiving the amount of blood they need to stay healthy and function properly.

A baby with a prenatally diagnosed cystic hygroma should be delivered in a major medical center equipped to deal with neonatal complications, such as a neonatal intensive care unit. An obstetrician usually decides the method of delivery. If the cystic hygroma is large, a cesarean section may be performed. After birth, infants with a persistent cystic hygroma must be monitored for airway obstruction. A thin needle may be used to reduce the volume of the cystic hygroma to prevent facial deformities and airway obstruction. Close observation of the baby by a neonatologist after birth is recommended. If resolution of the cystic hygroma does not occur before birth, a pediatric surgeon should be consulted.

Cystic hygromas that develop in the third trimester, after thirty weeks gestation, or in the postnatal period are usually not associated with chromosome abnormalities. There is a chance of recurrence after surgical removal of the cystic hygroma. The chance of recurrence depends on the extent of the cystic hygroma and whether its wall was able to be completely removed.

Treatments for removal of cystic hygroma are surgery or sclerosing agents which include:

- Bleomycin

- Doxycycline

- Ethanol (pure)

- Picibanil (OK-432)

- Sodium tetradecyl sulfate

In some communities mothers routinely push the small bulge back in and tape a coin over the palpable hernia hole until closure occurs. This practice is not medically recommended as there is a small risk of trapping a loop of bowel under part of the coin resulting in a small area of ischemic bowel. This "fix" does not help and germs may accumulate under the tape, causing infection. The use of bandages or other articles to continuously reduce the hernia is not evidence-based.

An umbilical hernia can be fixed in two different ways. The surgeon can opt to stitch the walls of the abdominal or he/she can place mesh over the opening and stitch it to the abdominal walls. The latter is of a stronger hold and is commonly used for larger defects in the abdominal wall. Most surgeons will not repair the hernia until 5–6 years after the baby is born. Most umbilical hernias in infants and children close spontaneously and rarely have complications of gastrointestinal-content incarcerations.

How far the projection of the swelling extends from the surface of the abdomen (the belly) varies from child to child. In some, it may be just a small protrusion; in others it may be a large rounded swelling that bulges out when the baby cries. It may hardly be visible when the child is quiet and or sleeping.

Normally, the abdominal muscles converge and fuse at the umbilicus during the formation stage, however, in some cases, there remains a gap where the muscles do not close and through this gap the inner intestines come up and bulge under the skin, giving rise to an umbilical hernia. The bulge and its contents can easily be pushed back and reduced into the abdominal cavity.

In contrast to an inguinal hernia, the complication incidence is very low, and in addition, the gap in the muscles usually closes with time and the hernia disappears on its own. The treatment of this condition is essentially conservative: observation allowing the child to grow up and see if it disappears. Operation and closure of the defect is required only if the hernia persists after the age of 3 years or if the child has an episode of complication during the period of observation like irreducibility, intestinal obstruction, abdominal distension with vomiting, or red shiny painful skin over the swelling. Surgery is always done under anesthesia. The defect in the muscles is defined and the edges of the muscles are brought together with sutures to close the defect. In general, the child needs to stay in the hospital for 2 days and the healing is complete within 8 days.

At times, there may be a fleshy red swelling seen in the hollow of the umbilicus that persists after the cord has fallen off. It may bleed on touch, or may stain the clothes that come in contact with it. This needs to be shown to a pediatric surgeon. This is most likely to be an umbilical polyp and the therapy is to tie it at the base with a stitch so that it falls off and there is no bleeding. Alternatively, it may be an umbilical granuloma that responds well to local application of dry salt or silver nitrate but may take a few weeks to heal and dry.

Modern therapy is aimed at surgical reconstruction of the bladder and genitalia. Both males and females are born with this anomaly. Treatment is similar.

In males treatments have been:

In the modern staged repair of exstrophy (MSRE) the initial step is closure of the abdominal wall, often requiring a pelvic osteotomy. This leaves the patient with penile epispadias and urinary incontinence. At approximately 2–3 years of age the patient then undergoes repair of the epispadias after testosterone stimulation. Finally, bladder neck repair usually occurs around the age of 4–5 years, though this is dependent upon a bladder with adequate capacity and, most importantly, an indication that the child is interested in becoming continent.

In the complete primary repair of exstrophy (CPRE) the bladder closure is combined with an epispadias repair, in an effort to decrease costs and morbidity. This technique has, however, led to significant loss of penile and corporal tissue, particularly in younger patients.

In females treatment has included:

Surgical reconstruction of the clitoris which is separated into two distinct bodies. Surgical reconstruction to correct the split of the mons, redefine the structure of the bladder neck and urethra. Vaginoplasty will correct the anteriorly displaced vagina. If the anus is involved, it is also repaired. Fertility remains and women who were born with bladder extrophy usually develop prolapse due to the weaker muscles of the pelvic floor.

Surgery is not always an option when the anatomy of the malformation creates too much of a risk. Recent improvements in endovascular procedures have made many cases, which were not surgically accessible, treatable. Endovascular treatments involve delivering drugs, balloons, or coils to the site of the malformation through blood vessels via catheters. These treatments work by limiting blood flow through the vein. There is, however, still risk of complications from endovascular treatments. The wall of the vein can be damaged during the procedure and, in some cases, the emboli can become dislodged and travel through the vascular system. Two-dimensional echocardiography with color-flow imaging and pulsed Doppler ultrasound was used to evaluate one fetus and five neonates with a Vein of Galen malformation. Color-flow imaging and pulsed Doppler ultrasonography provided anatomical and pathophysiological information regarding cardiac hemodynamics and intracranial blood flow; with the patient's clinical status, these methods provided a reliable, noninvasive means to evaluate the effectiveness of therapy and the need for further treatment in neonates with Vein of Galen malformations. When none of these procedures are viable, shunting can be used to ameliorate the pressure inside the varix. Seizures usually are managed with antiepileptic medications.

The use of orthotic bracing, pioneered by Sydney Haje as of 1977, is finding increasing acceptance as an alternative to surgery in select cases of pectus carinatum. In children, teenagers, and young adults who have pectus carinatum and are motivated to avoid surgery, the use of a customized chest-wall brace that applies direct pressure on the protruding area of the chest produces excellent outcomes. Willingness to wear the brace as required is essential for the success of this treatment approach. The brace works in much the same way as orthodontics (braces that correct the alignment of teeth). The brace consists of front and back compression plates that are anchored to aluminum bars. These bars are bound together by a tightening mechanism which varies from brace to brace. This device is easily hidden under clothing and must be worn from 14 to 24 hours a day. The wearing time varies with each brace manufacturer and the managing physicians protocol, which could be based on the severity of the carinatum malformation (mild moderate severe) and if it is symmetric or asymmetric.

Depending on the manufacturer and/or the patient's preference, the brace may be worn on the skin or it may be worn over a body 'sock' or sleeve called a Bracemate, specifically designed to be worn under braces. A physician or orthotist or brace manufacturer's representative can show how to check to see if the brace is in correct position on the chest.

Bracing is becoming more popular over surgery for pectus carinatum, mostly because it eliminates the risks that accompany surgery. The prescribing of bracing as a treatment for pectus carinatum has 'trickled down' from both paediatric and thoracic surgeons to the family physician and pediatricians again due to its lower risks and well-documented very high success results. The pectus carinatum guideline of 2012 of the American Pediatric Surgical Association has stated: "As reconstructive therapy for the compliant pectus [carinatum] malformation, nonoperative compressive orthotic bracing is usually an appropriate first line of therapy as it does not preclude the operative option. For appropriate candidates, orthotic bracing of chest wall malformations can reasonably be expected to prevent worsening of the malformation and often results in a lasting correction of the malformation. Orthotic bracing is often successful in prepubertal children whose chest wall is compliant. Expert opinion suggests that the noncompliant chest wall malformation or significant asymmetry of the pectus carinatum malformation caused by a concomitant excavatum-type malformation may not respond to orthotic bracing."

Regular supervision during the bracing period is required for optimal results. Adjustments may be needed to the brace as the child grows and the pectus improves.

Upon delivery, the exposed bladder is irrigated and a non-adherent film is placed to prevent as much contact with the external environment as possible. In the event the child was not born at a medical center with an appropriate exstrophy support team then transfer will likely follow. Upon transfer, or for those infants born at a medical center able to care for bladder exstrophy, imaging may take place in the first few hours of life prior to the child undergoing surgery.

Primary (immediate) closure is indicated only in those patients with a bladder of appropriate size, elasticity, and contractility as those patients are most likely to develop a bladder of adequate capacity after early surgical intervention.

Conditions that are absolute contraindications despite bladder adequacy include duplication of the penis or scrotum and significant bilateral hydronephrosis.

A systematic review of the evidence found that exercise may or may not reduce the size of the gap in pregnant or postpartum women. The authors looked at 8 studies totaling 336 women and concluded, “Due to the low number and quality of included articles, there is insufficient evidence to recommend that exercise may help to prevent or reduce DRAM” also stating that "non-specific exercise may or may not help to prevent or reduce DRAM during the ante- and postnatal periods."

Treatment for a diaphragmatic hernia usually involves surgery, with acute injuries often repaired with monofilament permanent sutures.

Treatment for sigmoid volvulus may include sigmoidoscopy. If the mucosa of the sigmoid looks normal and pink, place a rectal tube for decompression, correct any fluid, electrolyte, cardiac, renal or pulmonary abnormalities and then take the person to the operating room for repair. If surgery is not performed, there is a high rate of recurrence.

For people with signs of sepsis or an abdominal catastrophe, immediate surgery and resection is advised.

Treatment is surgical, potentially with a laparoscopic resection. In patients with bleeding, strangulation of bowel, bowel perforation or bowel obstruction, treatment involves surgical resection of both the Meckel's diverticulum itself along with the adjacent bowel segment, and this procedure is called a "small bowel resection". In patients without any of the aforementioned complications, treatment involves surgical resection of the Meckel's diverticulum only, and this procedure is called a simple diverticulectomy.

With regards to asymptomatic Meckel's diverticulum, some recommend that a search for Meckel's diverticulum should be conducted in every case of appendectomy/laparotomy done for acute abdomen, and if found, Meckel's diverticulectomy or resection should be performed to avoid secondary complications arising from it.

Management has three components: interventions before delivery, timing and place of delivery, and therapy after delivery.

In some cases, fetal therapy is available for the underlying condition; this may help to limit the severity of pulmonary hypoplasia. In exceptional cases, fetal therapy may include fetal surgery.

A 1992 case report of a baby with a sacrococcygeal teratoma (SCT) reported that the SCT had obstructed the outlet of the urinary bladder causing the bladder to rupture in utero and fill the baby's abdomen with urine (a form of ascites). The outcome was good. The baby had normal kidneys and lungs, leading the authors to conclude that obstruction occurred late in the pregnancy and to suggest that the rupture may have protected the baby from the usual complications of such an obstruction. Subsequent to this report, use of a vesicoamniotic shunting procedure (VASP) has been attempted, with limited success.

Often, a baby with a high risk of pulmonary hypoplasia will have a planned delivery in a specialty hospital such as (in the United States) a tertiary referral hospital with a level 3 neonatal intensive-care unit. The baby may require immediate advanced resuscitation and therapy.

Early delivery may be required in order to rescue the fetus from an underlying condition that is causing pulmonary hypoplasia. However, pulmonary hypoplasia increases the risks associated with preterm birth, because once delivered the baby requires adequate lung capacity to sustain life. The decision whether to deliver early includes a careful assessment of the extent to which delaying delivery may increase or decrease the pulmonary hypoplasia. It is a choice between expectant management and active management. An example is congenital cystic adenomatoid malformation with hydrops; impending heart failure may require a preterm delivery. Severe oligohydramnios of early onset and long duration, as can occur with early preterm rupture of membranes, can cause increasingly severe PH; if delivery is postponed by many weeks, PH can become so severe that it results in neonatal death.

After delivery, most affected babies will require supplemental oxygen. Some severely affected babies may be saved with extracorporeal membrane oxygenation (ECMO). Not all specialty hospitals have ECMO, and ECMO is considered the therapy of last resort for pulmonary insufficiency. An alternative to ECMO is high-frequency oscillatory ventilation.

In extreme cases, diastasis recti is corrected during the cosmetic surgery procedure known as an abdominoplasty by creating a plication or folding of the linea alba and suturing together. This creates a tighter abdominal wall.

In adult females, a laparoscopic "Venetian blind" technique can be used for plication of the recti.