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.

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

While there is no current cure, the treatments for Chiari malformation are surgery and management of symptoms, based on the occurrence of clinical symptoms rather than the radiological findings. The presence of a syrinx is known to give specific signs and symptoms that vary from dysesthetic sensations to algothermal dissociation to spasticity and paresis. These are important indications that decompressive surgery is needed for patients with Chiari Malformation Type II. Type II patients have severe brain stem damage and rapidly diminishing neurological response.

Decompressive surgery involves removing the lamina of the first and sometimes the second or third cervical vertebrae and part of the occipital bone of the skull to relieve pressure. The flow of spinal fluid may be augmented by a shunt. Since this surgery usually involves the opening of the dura mater and the expansion of the space beneath, a dural graft is usually applied to cover the expanded posterior fossa.

A small number of neurological surgeons believe that detethering the spinal cord as an alternate approach relieves the compression of the brain against the skull opening (foramen magnum), obviating the need for decompression surgery and associated trauma. However, this approach is significantly less documented in the medical literature, with reports on only a handful of patients. It should be noted that the alternative spinal surgery is also not without risk.

Complications of decompression surgery can arise. They include bleeding, damage to structures in the brain and spinal canal, meningitis, CSF fistulas, occipito-cervical instability and pseudomeningeocele. Rare post-operative complications include hydrocephalus and brain stem compression by retroflexion of odontoid. Also, an extended CVD created by a wide opening and big duroplasty can cause a cerebellar "slump". This complication needs to be corrected by cranioplasty.

In certain cases, irreducible compression of the brainstem occurs from in front (anteriorly or ventral) resulting in a smaller posterior fossa and associated Chiari malformation. In these cases, an anterior decompression is required. The most commonly used approach is to operate through the mouth (transoral) to remove the bone compressing the brainstem, typically the odontoid. This results in decompressing the brainstem and therefore gives more room for the cerebellum, thus decompressing the Chiari malformation. Arnold Menzes, MD, is the neurosurgeon who pioneered this approach in the 1970s at the University of Iowa. Between 1984 and 2008 (the MR imaging era), 298 patients with irreducible ventral compression of the brainstem and Chiari type 1 malformation underwent a transoral approach for ventral cervicomedullary decompression at the University of Iowa. The results have been excellent resulting in improved brainstem function and resolution of the Chiari malformation in the majority of patients.

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.

Treatment for Klippel–Feil syndrome is symptomatic and may include surgery to relieve cervical or craniocervical instability and constriction of the spinal cord, and to correct scoliosis.

Failing non-surgical therapies, spinal surgery may provide relief. Adjacent segment disease and scoliosis are two examples of common symptoms associated with Klippel–Feil syndrome, and they may be treated surgically. The three categories treated for types of spinal cord deficiencies are massive fusion of the cervical spine (Type I), the fusion of 1 or 2 vertebrae (Type II), and the presence of thoracic and lumbar spine anomalies in association with type I or type II Klippel–Feil syndrome (Type III).

Adjacent segment disease can be addressed by performing cervical disc arthroplasty using a device such as the Bryan cervical disc prosthesis.

The option of the surgery is to maintain range of motion and attenuate the rate of adjacent segment disease advancement without fusion.

Another type of arthroplasty that is becoming an alternate choice to spinal fusion is Total Disc Replacement. Total disc replacement objective is to reduce pain or eradicate it.

Spinal fusion is commonly used to correct spinal deformities such as scoliosis. Arthrodesis is the last resort in pain relieving procedures, usually when arthroplasties fail.

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.

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.

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.

For patients with severe pectus carinatum, surgery may be necessary. However bracing could and may still be the first line of treatment. Some severe cases treated with bracing may result in just enough improvement that patient is happy with the outcome and may not want surgery afterwards.

If bracing should fail for whatever reason then surgery would be the next step. The two most common procedures are the Ravitch technique and the Reverse Nuss procedure.

A modified Ravitch technique uses bioabsorbable material and postoperative bracing, and in some cases a diced rib cartilage graft technique.

The Nuss was developed by Donald Nuss at the Children's Hospital of the King's Daughters in Norfolk, Va. The Nuss is primarily used for Pectus Excavatum, but has recently been revised for use in some cases of PC, primarily when the malformation is symmetrical.

The heterogeneity of the Klippel–Feil syndrome has made it difficult to outline the diagnosis as well as the prognosis classes for this disease. Because of this, it has complicated the exact explanation of the genetic cause of the syndrome.

The prognosis for most individuals with KFS is good if the disorder is treated early on and appropriately. Activities that can injure the neck should be avoided, as it may contribute to further damage. Other diseases associated with the syndrome can be fatal if not treated, or if found too late to be treatable.

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 traditional medical management of scoliosis is complex and is determined by the severity of the curvature and skeletal maturity, which together help predict the likelihood of progression.

The conventional options for children and adolescents are:

1. Observation

2. Bracing

3. Surgery

For adults, treatment usually focuses on relieving any pain:

1. Painkilling medication

2. Bracing

3. Surgery

Treatment for idiopathic scoliosis also depends upon the severity of the curvature, the spine’s potential for further growth, and the risk that the curvature will progress. Mild scoliosis (less than 30 degrees deviation) may simply be monitored and treated with exercise. Moderately severe scoliosis (30–45 degrees) in a child who is still growing may require bracing. Severe curvatures that rapidly progresses may be treated surgically with spinal rod placement. Bracing may prevent a progressive curvature, but evidence for this is not very strong. In all cases, early intervention offers the best results.

A growing body of scientific research testifies to the efficacy of specialized treatment programs of physical therapy, which may include bracing.

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

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.

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.

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.

Treatment is surgical with attention to form and volume. Surgery usually takes place before the age of one since it has been reported that the intellectual outcome is better.

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

The treatment of arterial tortuosity syndrome entails possible surgery for aortic aneurysms, as well as, follow ups which should consist of EGC. The prognosis of this condition has it at about 12% mortality

The only treatment for this disorder is surgery to reduce the compression of cranial nerves and spinal cord. However, bone regrowth is common since the surgical procedure can be technically difficult. Genetic counseling is offered to the families of the people with this disorder.

Usually the sequestration is removed after birth via surgery. In most cases this surgery is safe and effective; the child will grow up to have normal lung function.

In a few instances, fetuses with sequestrations develop problematic fluid collections in the chest cavity. In these situations a Harrison catheter shunt can be used to drain the chest fluid into the amniotic fluid.

In rare instances where the fetus has a very large lesion, resuscitation after delivery can be dangerous. In these situations a specialized delivery for management of the airway compression can be planned called the EXIT procedure, or a fetal laser ablation procedure can be performed. During this minimally invasive fetal intervention, a small needle is inserted into the sequestration, and a laser fiber is targeted at the abnormal blood vessel going to the sequestration. The goal of the operation is to use laser energy to stop the blood flow to the sequestration, causing it to stop growing. Ideally, after the surgery, the sequestration steals less blood flow from the fetus, and the heart and lungs start growing more normally as the sequestration shrinks in size and the pleural effusion goes away.

The treatment for this is a wedge resection, segmentectomy, or lobectomy via a VATS procedure or thoracotomy.

Pulmonary sequestrations usually get their blood supply from the thoracic aorta.

Since the diaphragm is in constant motion with respiration, and because it is under tension, lacerations will not heal on their own. Surgery is needed to repair a torn diaphragm. Most of the time, the injury is repaired during laparotomy. Other injuries, such as hemothorax, may present a more immediate threat and may need to be treated first if they accompany diaphragmatic rupture. Video-assisted thoracoscopy may be used.

Bracing is normally done when the person has bone growth remaining and is, in general, implemented to hold the curve and prevent it from progressing to the point where surgery is recommended. In some cases with juveniles, bracing has reduced curves significantly, going from a 40 degrees (of the curve, mentioned in length above) out of the brace to 18 degrees in it. Braces are sometimes prescribed for adults to relieve pain related to scoliosis. Bracing involves fitting the patient with a device that covers the torso; in some cases, it extends to the neck. The most commonly used brace is a TLSO, such as a Boston brace, a corset-like appliance that fits from armpits to hips and is custom-made from fiberglass or plastic. It is sometimes worn 22–23 hours a day, depending on the doctor's prescription, and applies pressure on the curves in the spine. The effectiveness of the brace depends on not only brace design and orthotist skill but also patient compliance and amount of wear per day.

The typical use of braces is for idiopathic curves that are not grave enough to warrant surgery, but they may also be used to prevent the progression of more severe curves in young children, to buy the child time to grow before performing surgery, which would prevent further growth in the part of the spine affected.

Indications for bracing: people who are still growing who present with Cobb angles less than 20 degrees should be closely monitored. People who are still growing who present with Cobb angles of 20 degrees to 29 degrees should be braced according to the risk of progression by considering age, Cobb angle increase over a six-month period, Risser sign, and clinical presentation. People who are still growing who present with Cobb angles greater than 30 degrees should be braced. However, these are guidelines and not every person will fit into this table. For example, a person who is still growing with a 17-degree Cobb angle and significant thoracic rotation or flatback could be considered for nighttime bracing. On the opposite end of the growth spectrum, a 29-degree Cobb angle and a Risser sign three or four might not need to be braced because there is reduced potential for progression. The Scoliosis Research Society's recommendations for bracing include curves progressing to larger than 25°, curves presenting between 30 and 45°, Risser sign 0, 1, or 2 (an X-ray measurement of a pelvic growth area), and less than six months from the onset of menses in girls.

Scoliosis braces are usually comfortable, especially when well designed and well fitted, also after the 7- to 10-day break-in period. A well fitted and functioning scoliosis brace provides comfort when it is supporting the deformity and redirecting the body into a more corrected and normal physiological position.

Evidence supports that bracing prevents worsening of disease but it is unclear whether it changes quality of life, appearance, or back pain.

The primary goal in surgical intervention is to allow normal cranial vault development to occur. This can be achieved by excision of the prematurely fused suture and correction of the associated skull deformities. If the synostosis goes uncorrected, the deformity will progressively worsen not only threatening the aesthetic aspect, but also the functional aspect. This is especially the case in the asymmetric conditions, such as unilateral coronal synostosis, with compromised function of the eyes and the jaw.

In addition signs of compromised neurodevelopment have been seen amongst all the synostoses, although this may also be caused by primary maldevelopment of the brain and can thus not be prevented by surgical intervention.

There are a few basic elements involved in the surgical intervention aimed at normalization of the cranial vault.

- One is minimization of blood loss, which is attempted by injection of vasoconstrictive agents (i.e. epinephrine) seven to ten minutes before scalp incision. In addition is the initiation of surgery delayed until blood products are physically present in the operating room.

- Another general agreement is the avoidance of the use of titanium plates in the fixation of the skull. The complication following this procedure is gradual movement of the titanium plates towards the brain, induced by resorption of the innermost bone layer of the skull and deposition of new bone on the outermost layer, thereby integrating the titanium plates. In some cases, the plates were even seen coming in direct contact with the brain. Absorbable plates are now used instead.