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.

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.

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.

Treatments of NTDs depends on the severity of the complication. No treatment is available for anencephaly and infants usually do not survive more than a few hours. Aggressive surgical management has improved survival and the functions of infants with spina bifida, meningoceles and mild myelomeningoceles. The success of surgery often depends on the amount of brain tissue involved in the encephalocele. The goal of treatment for NTDs is to allow the individual to achieve the highest level of function and independence. Fetal surgery in utero before 26 weeks gestation has been performed with some hope that there is benefit to the final outcome including a reduction in Arnold–Chiari malformation and thereby decreases the need for a ventriculoperitoneal shunt but the procedure is very high risk for both mother and baby and is considered extremely invasive with questions that the positive outcomes may be due to ascertainment bias and not true benefit. Further, this surgery is not a cure for all problems associated with a neural tube defect. Other areas of research include tissue engineering and stem cell therapy but this research has not been used in humans.

These hernias should be repaired because of the high risk of strangulation; fortunately, surgery is straightforward, with only larger defects requiring a mesh prosthesis. Varied Spigelian hernia mesh repair techniques have been described, although evidence suggests laparoscopy results in less morbidity and shorter hospitalization compared with open procedures. Mesh-free laparoscopic suture repair is feasible and safe. This novel uncomplicated approach to small Spigelian hernias combines the benefits of laparoscopic localization, reduction, and closure without the morbidity and cost associated with foreign material.

No treatment is needed for correcting lung hernias. Some surgeons offer cosmetic surgery to remove the protruding mass.

Symptomatic epigastric hernias are repaired with surgery. Even if they are asymptomatic, they can be surgically corrected for cosmetic reasons. In general, cosmetic surgery on infants is delayed until the infant is older and better able to tolerate anaesthesia.

Pregnant mothers are advised to take folic acid supplements to reduce risk of iniencephaly by up to 70%. Pregnant mothers are also advised not to take antiepileptic drugs, diuretics, antihistamines, and sulfa drugs, all of which have been associated with increased risk for neural tube defects.

Some surgeons choose to perform "key-hole" or laparoscopic surgery (also called minimally invasive surgery) rather than conventional "open" surgery. With minimally invasive surgery, one or more small incisions are made that allow the surgeon to use a surgical camera and small tools to repair the hernia.

Either open or minimally invasive surgery may be performed under general or regional anaesthesia, depending on the extent of the intervention needed. Three approaches have been described for open surgery.

- Lockwood’s infra-inguinal approach

- Lotheissen‘s trans-inguinal approach

- McEvedy’s high approach

The infra-inguinal approach is the preferred method for elective repair. The trans-inguinal approach involves dissecting through the inguinal canal and carries the risk of weakening the inguinal canal. McEvedy’s approach is preferred in the emergency setting when strangulation is suspected. This allows better access to and visualisation of bowel for possible resection. In any approach, care should be taken to avoid injury to the urinary bladder which is often a part of the medial part of the hernial sac.

Repair is either performed by suturing the inguinal ligament to the pectineal ligament using strong non-absorbable sutures or by placing a mesh plug in the femoral ring. With either technique care should be taken to avoid any pressure on the femoral vein.

Femoral hernias, like most other hernias, usually need operative intervention. This should ideally be done as an elective (non-emergency) procedure. However, because of the high incidence of complications, femoral hernias often need emergency surgery.

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.).

Surgical correction of inguinal hernias is called a hernia repair. It is not recommended in minimally symptomatic hernias, for which watchful waiting is advised, due to the risk of post herniorraphy pain syndrome. Surgery is commonly performed as outpatient surgery. There are various surgical strategies which may be considered in the planning of inguinal hernia repair. These include the consideration of mesh use (e.g. synthetic or biologic), open repair, use of laparoscopy, type of anesthesia (general or local), appropriateness of bilateral repair, etc. Laparoscopy is most commonly used for non-emergency cases, however, a minimally invasive open repair may have a lower incidence of post-operative nausea and mesh associated pain. During surgery conducted under local anaesthesia, the patient will be asked to cough and strain during the procedure to help in demonstrating that the repair is without tension and sound.

Constipation after hernia repair results in strain to evacuate the bowel causing pain, and fear that the sutures may rupture. Opioid analgesia makes constipation worse. Promoting an easy bowel motion is important post-operatively.

Surgical correction is always recommended for inguinal hernias in child.

Emergency surgery for incarceration and strangulation carry much higher risk than planned, "elective" procedures. However, the risk of incarceration is low, evaluated at 0.2% per year. On the other hand, surgery has a risk of inguinodynia (10-12%), and this is why males with minimal symptoms are advised to watchful waiting. However, if they experience discomfort while doing physical activities or they routinely avoid them by the fear of pain, they should seek surgical evaluation. For female patients, surgery is recommended even for asymptomatic patients.

In 1996, the United States Food and Drug Administration published regulations requiring the addition of folic acid to enriched breads, cereals, flour and other grain products. It is important to note that during the first four weeks of pregnancy (when most women do not even realize that they are pregnant), adequate folate intake is essential for proper operation of the neurulation process. Therefore, women who could become pregnant are advised to eat foods fortified with folic acid or take supplements in addition to eating folate-rich foods to reduce the risks of serious birth defects.

In Canada, mandatory fortification of selected foods with folic acid has been shown to reduce the incidence of neural tube defects by 46%.

Women who may become pregnant are advised to get 400 micrograms of folic acid daily. Women who have previously given birth to a child with a neural tube defect may benefit from a supplement containing 4.0 mg/5.0 mg in the UK mg daily, following advice provided by their doctor.

In the great majority of cases, sufferers experience no life-altering discomfort, and no treatment is required. If there is pain or discomfort, 3 or 4 sips of room temperature water will usually relieve the pain. Symptomatic patients should elevate the head of their beds and avoid lying down directly after meals. If the condition has been brought on by stress, stress reduction techniques may be prescribed, or if overweight, weight loss may be indicated. Antisecretory drugs like proton pump inhibitors and H receptor blockers can be used to reduce acid secretion. Medications that reduce the lower esophageal sphincter (LES) pressure should be avoided.

However, in some unusual instances, as when the hiatal hernia is unusually large, or is of the paraesophageal type, it may cause esophageal stricture or severe discomfort. About 5% of hiatus hernias are paraesophageal. If symptoms from such a hernia are severe for example if chronic acid reflux threatens to severely injure the esophagus or is causing Barrett's esophagus, surgery is sometimes recommended. However surgery has its own risks including death and disability, so that even for large or paraesophageal hernias, watchful waiting may on balance be safer and cause fewer problems than surgery. Complications from surgical procedures to correct a hiatus hernia may include gas bloat syndrome, dysphagia (trouble swallowing), dumping syndrome, excessive scarring, and rarely, achalasia. Surgical procedures sometimes fail over time, requiring a second surgery to make repairs.

One surgical procedure used is called Nissen fundoplication. In fundoplication, the gastric fundus (upper part) of the stomach is wrapped, or plicated, around the inferior part of the esophagus, preventing herniation of the stomach through the hiatus in the diaphragm and the reflux of gastric acid. The procedure is now commonly performed laparoscopically. With proper patient selection, laparoscopic fundoplication recent studies have indicated relatively low complication rates, quick recovery, and relatively good long term results.

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.

The complete or partial absence of the pectoralis muscle is the malformation that defines Poland Syndrome. It can be treated by inserting a custom implant designed by CAD (computer aided design). A 3D reconstruction of the patient's chest is performed from a medical scanner to design a virtual implant perfectly adapted to the anatomy of each one. The implant is made of medical silicone unbreakable rubber. This treatment is purely cosmetic and does not make up for the patient's imbalanced upper body strength.

The Poland syndrome malformations being morphological, correction by custom implant is a first-line treatment. This technique allows a wide variety of patients to be treated with good outcomes. Poland Syndrome can be associated with bones, subcutaneous and mammary atrophy: if the first, as for pectus excavatum, is successfully corrected by a custom implant, the others can require surgical intervention such as lipofilling or silicone breast implant, in a second operation.

The surgery takes place under general anaesthesia and lasts less than 1 hour. The surgeon prepares the locus to the size of the implant after performing a 8-cm axillary incision and inserts the implant beneath the skin. The closure is made in 2 planes.

The implant will replace the pectoralis major muscle, thus enabling the thorax to be symmetrical and, in women, the breast as well. If necessary, especially in the case of women, a second operation will complement the result by the implantation of a breast implant and / or lipofilling.

Lipomodelling is progressively used in the correction of breast and chest wall deformities. In Poland syndrome, this technique appears to be a major advance that will probably revolutionize the treatment of severe cases. This is mainly due to its ability to achieve previously unachievable quality of reconstruction with minimal scaring.

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.

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.

Traditional "open" repair of incisional hernias can be quite difficult and complicated. The weakened tissue of the abdominal wall is re-incised and a repair is reinforced using a prosthetic mesh. Complications, particularly infection of the incision, frequently occur because of the large size of the incision required to perform this surgery. A mesh infection after this type of hernia repair most frequently requires a complete removal of the mesh and ultimately results in surgical failure. In addition, large incisions required for open repair are commonly associated with significant postoperative pain. Reported recurrence rates after open repair are up to 20% and influenced by mesh size and fixation type.

Laparoscopic incisional hernia repair is a new method of surgery for this condition. The operation is performed using surgical microscopes and specialized instruments. The surgical mesh is placed into the abdomen underneath the abdominal muscles through small incisions to the side of the hernia. In this manner, the weakened tissue of the original hernia is never re-incised to perform the repair, and one can minimize the potential for wound complications such as infections. In addition, performance of the operation through smaller incisions can make the operation less painful and speed recovery. Laparoscopic repair has been demonstrated to be safe and a more resilient repair than open incisional hernia repair.

There is currently no medical recommendation about how to manage an inguinal hernia condition in adults, due to the fact that, until recently, elective surgery used to be recommended. The hernia truss is intended to contain a reducible inguinal hernia within the abdomen. It is not considered to provide a cure, and if the pads are hard and intrude into the hernia aperture they may cause scarring and enlargement of the aperture. In addition, most trusses with older designs are not able effectively to contain the hernia at all times, because their pads do not remain permanently in contact with the hernia. The more modern variety of truss is made with non-intrusive flat pads and comes with a guarantee to hold the hernia securely during all activities. Although there is as yet no proof that such devices can prevent an inguinal hernia from progressing, they have been described by users as providing greater confidence and comfort when carrying out physically demanding tasks. A truss also increases the probability of complications, which include strangulation of the hernia, atrophy of the spermatic cord, and atrophy of the fascial margins. This allows the defect to enlarge and makes subsequent repair more difficult. Their popularity is likely to increase, as many individuals with small, painless hernias are now delaying hernia surgery due to the risk of post-herniorrhaphy pain syndrome. The elasticised pants used by athletes also provide useful support for the smaller hernia.

Since newborns with iniencephaly so rarely survive past childbirth, a standard treatment does not exist.

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.

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

There is no standard treatment for hydranencephaly. Treatment is symptomatic and supportive. Hydrocephalus may be treated with surgical treatment of a shunt, which often grants a much better prognosis and greater quality of life.

The prognosis for children with hydranencephaly is generally quite poor. Death often occurs in the first year of life, but other children may live several years.

Medical text identifies that hydranencephalic children simply have only their brain stem function remaining, thus leaving formal treatment options as symptomatic and supportive. Severe hydrocephalus causing macrocephaly, a larger than average head circumference, can easily be managed by placement of a shunt and often displays a misdiagnosis of another lesser variation of cephalic condition due to the blanketing nature of hydrocephalus. Plagiocephaly, the asymmetrical distortion of the skull, is another typical associated condition that is easily managed through positioning and strengthening exercises to prevent torticollis, a constant spasm or extreme tightening of the neck muscles.