The timing of surgical interventions is debatable. Parents have to decide about their child in a very vulnerable time of their parenthood. Indications for early treatment are progressive deformities, such as syndactyly between index and thumb or transverse bones between the digital rays. Other surgical interventions are less urgent and can wait for 1 or 2 years.

When surgery is indicated, the choice of treatment is based on the classification. Table 4 shows the treatment of cleft hand divided into the classification of Manske and Halikis.

Techniques described by Ueba, Miura and Komada and the procedure of Snow-Littler are guidelines; since clinical and anatomical presentation within the types differ, the actual treatment is based on the individual abnormality.

Table 4: Treatment based on the classification of Manske and Halikis

Lip pits may be surgically removed either for aesthetic reasons or discomfort due to inflammation caused by bacterial infections or chronic saliva excretion, though spontaneous shrinkage of the lip pits has occurred in some rare cases. Chronic inflammation has also been reported to cause squamous-cell carcinoma. It is essential to completely remove the entire lip pit canal, as mucoid cysts can develop if mucous glands are not removed. A possible side effect of removing the lip pits is a loose lip muscle. Other conditions associated with VWS, including CL, CP, congenital heart defects, etc. are surgically corrected or otherwise treated as they would be if they were non-syndromic.

In general, there is no treatment available for CMTC, although associated abnormalities can be treated. In the case of limb asymmetry, when no functional problems are noted, treatment is not warranted, except for an elevation device for the shorter leg.

Laser therapy has not been successful in the treatment of CMTC, possibly due to the presence of many large and deep capillaries and dilated veins. Pulsed-dye laser and long-pulsed-dye laser have not yet been evaluated in CMTC, but neither argon laser therapy nor YAG laser therapy has been helpful.

When ulcers develop secondary to the congenital disease, antibiotic treatment such as oxacillin and gentamicin administered for 10 days has been prescribed. In one study, the wound grew Escherichia coli while blood cultures were negative.

There is no cure for ONH; however, many therapeutic interventions exist for the care of its symptoms. These may include hormone replacement therapy for hypopituitarism, occupational, physical, and/or speech therapy for other issues, and services of a teacher of students with blindness/visually impairment. Special attention should be paid to early development of oral motor skills and acclimation to textured foods for children with texture aversion, or who are otherwise resistant to eating.

Sleep dysfunction can be ameliorated using melatonin in the evening in order to adjust a child's circadian clock.

Treatment for strabismus may include patching of the better eye, which may result in improved vision in the worse eye; however, this should be reserved for cases in which the potential for vision improvement in both eyes is felt to be good. Surgery to align the eyes can be performed once children with strabismus develop equal visual acuity in both eyes, most often after the age of three. Generally surgery results in improved appearance only and not in improved visual function.

Harlequin syndrome is not debilitating so treatment is not normally necessary. In cases where the individual may feel socially embarrassed, contralateral sympathectomy may be considered, although compensatory flushing and sweating of other parts of the body may occur. In contralateral sympathectomy, the nerve bundles that cause the flushing in the face are interrupted. This procedure causes both sides of the face to no longer flush or sweat. Since symptoms of Harlequin syndrome do not typically impair a person’s daily life, this treatment is only recommended if a person is very uncomfortable with the flushing and sweating associated with the syndrome.

Children who develop severe bowing before the age of 3 may be treated with knee ankle foot orthoses. However, bracing may fail, or bowing may not be detected until the child is older. In some cases, surgery may be performed. Surgery may involve cutting the shin bone (tibia) to realign it, and sometimes lengthen it as well.

Other times, the growth of just the outer half of the tibia can be surgically restricted to allow the child’s natural growth to reverse the bowing process. This second, much smaller surgery is most effective in children with less severe bowing and significant growth remaining.

Return to normal function and cosmetic appearance is expected if the knee can be properly aligned.

Depending on the severity of the deformities, the treatment may include the amputation of the foot or part of the leg, lengthening of the femur, extension prosthesis, or custom shoe lifts. Amputation usually requires the use of prosthesis. Another alternative is a rotationplasty procedure, also known as Van Ness surgery. In this situation the foot and ankle are surgically removed, then attached to the femur. This creates a functional "knee joint". This allows the patient to be fit with a below knee prosthesis vs a traditional above knee prosthesis.

In less severe cases, the use of an Ilizarov apparatus can be successful in conjunction with hip and knee surgeries (depending on the status of the femoral head/kneecap) to extend the femur length to normal ranges. This method of treatment can be problematic in that the Ilizarov might need to be applied both during early childhood (to keep the femur from being extremely short at the onset of growth) and after puberty (to match leg lengths after growth has ended). The clear benefit of this approach, however, is that no prosthetics are needed and at the conclusion of surgical procedures the patient will not be biologically or anatomically different from a person born without PFFD.

Treatment for children with Blount's disease is typically braces but surgery may also be necessary, especially for teenagers. The operation consists of removing a piece of tibia, breaking the fibula and straightening out the bone; there is also a choice of elongating the legs. If not treated early enough, the condition worsens quickly.

The age when outer ear surgery can be attempted depends upon the technique chosen. The earliest is 7 for Rib Cartilage Grafts. However, some surgeons recommend waiting until a later age, such as 8–10 when the ear is closer to adult size. External ear prostheses have been made for children as young as 5.

For auricular reconstruction, there are several different options:

1. "Rib Cartilage Graft Reconstruction:" This surgery may be performed by specialists in the technique. It involves sculpting the patient's own rib cartilage into the form of an ear. Because the cartilage is the patient's own living tissue, the reconstructed ear continues to grow as the child does. In order to be sure that the rib cage is large enough to provide the necessary donor tissue, some surgeons wait until the patient is 8 years of age; however, some surgeons with more experience with this technique may begin the surgery on a child aged six. The major advantage of this surgery is that the patient's own tissue is used for the reconstruction. This surgery varies from two to four stages depending on the surgeon's preferred method. A novel one stage ear reconstruction technique is performed by a few select surgeons. One team is able to reconstruct the entire external ear and ear canal in one operation.

2. "Reconstruct the ear using a polyethylene plastic implant (also called Medpor):" This is a 1–2 stage surgery that can start at age 3 and can be done as an outpatient without hospitalization. Using the porous framework, which allows the patient's tissue to grow into the material and the patient's own tissue flap, a new ear is constructed in a single surgery. A small second surgery is performed in 3–6 months if needed for minor adjustments. This surgery should only be performed by experts in the techniques involved. The use of porous polyethylene implants for ear reconstruction was initiated in the 1980s by Alexander Berghaus.

3. "Ear Prosthesis:" An auricular (ear) prosthesis is custom made by an anaplastologist to mirror the other ear. Prosthetic ears can appear very realistic. They require a few minutes of daily care. They are typically made of silicone, which is colored to match the surrounding skin and can be attached using either adhesive or with titanium screws inserted into the skull to which the prosthetic is attached with a magnetic or bar/clip type system. These screws are the same as the BAHA (bone anchored hearing aid) screws and can be placed simultaneously. The biggest advantage over any surgery is having a prosthetic ear that allows the affected ear to appear as normal as possible to the natural ear. The biggest disadvantage is the daily care involved and knowing that the prosthesis is not real.

There are four levels (or "types") of malformation. The least severe indicates partial deformation (unilateral) of the sacrum. The second level indicates a bilateral (uniform) deformation. The most severe types involve a total absence of the sacrum.

Depending on the type of sacral agenesis, bowel or urinary bladder deficiencies may be present. A permanent colostomy may be necessary in the case of imperforate anus. Incontinence may also require some type of continence control system (e.g., self-catheterization) be utilized. Occasionally if deformities of the knees, legs or feet would prove unresponsive to corrective action, amputation at the knee may be proposed.

Before more comprehensive medical treatment was available, full amputation of the legs at the hip was often performed. More recently, the 'amputation' (actually a disarticulation because no cutting of the bone is involved) is done at the knee for those who have bent knee positions and webbing between thigh and calf to enable more ease of mobility and better seating. Some children with knee disarticulation use prosthetic legs to walk. Prosthetics for children without substantial hip and trunk control is usually abandoned in favor of faster and easier wheelchair mobility as the child's weight and age increases. Children may 'walk' on their hands and generally are able to climb and move about to accomplish whatever they need and want to accomplish. Children more mildly affected may have normal gait and no need for assistive devices for walking. Others may walk with bracing or crutches.

There is typically no cognitive impairment associated with this disability. Adults with this disability live independently, attend college, and have careers in various fields. In 2012, Spencer West, a man with sacral agenesis and both legs amputated, climbed Mt. Kilimanjaro using only his hands.

Incisions across the groove turned out to be ineffective. Excision of the groove followed by z-plasty could relieve pain and prevent autoamputation in Grade I and Grade II lesions. Grade III lesions are treated with disarticulating the metatarsophalangeal joint. This also relieves pain, and all patients have a useful and stable foot. Intralesional injection of corticosteroids is also helpful.

There is no pharmacological treatment for Roussy–Lévy syndrome.

Treatment options focus on palliative care and corrective therapy. Patients tend to benefit greatly from physical therapy (especially water therapy as it does not place excessive pressure on the muscles), while moderate activity is often recommended to maintain movement, flexibility, muscle strength and endurance.

Patients with foot deformities may benefit from corrective surgery, which, however, is usually a last resort. Most such surgeries include straightening and pinning the toes, lowering the arch, and sometimes, fusing the ankle joint to provide stability. Recovering from these surgeries is oftentimes long and difficult. Proper foot care including custom-made shoes and leg braces may minimize discomfort and increase function.

While no medicines are reported to treat the disorder, patients are advised to avoid certain medications as they may aggravate the symptoms.

Generally, no treatment is required for idiopathic presentation as it is a normal anatomical variant in young children. Treatment is indicated when it persists beyond 3 and a half years old. In the case of unilateral presentation or progressive worsening of the curvature, when caused by rickets, the most important thing is to treat the constitutional disease, at the same time instructing the care-giver never to place the child on its feet. In many cases this is quite sufficient in itself to effect a cure, but matters can be hastened somewhat by applying splints. When the deformity arises in older patients, either from trauma or occupation, the only permanent treatment is surgery, but orthopaedic bracing can provide relief.

Treatment is usually with some combination of the Ponseti or French methods. The Ponseti method includes the following: casting together with manipulation, cutting the Achilles tendon, and bracing. The Ponseti method has been found to be effective in correcting the problem in those under the age of two. The French method involves realignment and tapping of the foot is often effective but requires a lot of effort by caregivers. Another technique known as Kite does not appear as good. In about 20% of cases further surgery is required.

Typically, testing is first done to determine the quality of hearing. This can be done as early as in the first two weeks with a BAER test (Brain Stem Auditory Response Test). At age 5–6, CT or CAT scans of the middle ear can be done to elucidate its development and clarify which patients are appropriate candidates for surgery to improve hearing. For younger individuals, this is done under sedation.

The hearing loss associated with congenital aural atresia is a conductive hearing loss—hearing loss caused by inefficient conduction of sound to the inner ear. Essentially, children with aural atresia have hearing loss because the sound cannot travel into the (usually) healthy inner ear—there is no ear canal, no eardrum, and the small ear bones (malleus/hammer, incus/anvil, and stapes/stirrup) are underdeveloped. "Usually" is in parentheses because rarely, a child with atresia also has a malformation of the inner ear leading to a sensorineural hearing loss (as many as 19% in one study). Sensorineural hearing loss is caused by a problem in the inner ear, the cochlea. Sensorineural hearing loss is not correctable by surgery, but properly fitted and adjusted hearing amplification (hearing aids) generally provide excellent rehabilitation for this hearing loss. If the hearing loss is severe to profound in both ears, the child may be a candidate for a cochlear implant (beyond the scope of this discussion).

Unilateral sensorineural hearing loss was not generally considered a serious disability by the medical establishment before the nineties; it was thought that the afflicted person was able to adjust to it from birth. In general, there are exceptional advantages to gain from an intervention to enable hearing in the microtic ear, especially in bilateral microtia. Children with untreated unilateral sensorineural hearing loss are more likely to have to repeat a grade in school and/or need supplemental services (e.g., FM system – see below) than their peers.

Children with unilateral sensorineural hearing loss often require years of speech therapy in order to learn how to enunciate and understand spoken language. What is truly unclear, and the subject of an ongoing research study, is the effect of unilateral conductive hearing loss (in children with unilateral aural atresia) on scholastic performance. If atresia surgery or some form of amplification is not used, special steps should be taken to ensure that the child is accessing and understanding all of the verbal information presented in school settings. Recommendations for improving a child's hearing in the academic setting include preferential seating in class, an FM system (the teacher wears a microphone, and the sound is transmitted to a speaker at the child's desk or to an ear bud or hearing aid the child wears), a bone-anchored hearing aid (BAHA), or conventional hearing aids. Age for BAHA implantation depends on whether the child is in Europe (18 months) or the US (age 5). Until then it is possible to fit a BAHA on a softband

It is important to note that not all children with aural atresia are candidates for atresia repair. Candidacy for atresia surgery is based on the hearing test (audiogram) and CT scan imaging. If a canal is built where one does not exist, minor complications can arise from the body's natural tendency to heal an open wound closed. Repairing aural atresia is a very detailed and complicated surgical procedure which requires an expert in atresia repair. While complications from this surgery can arise, the risk of complications is greatly reduced when using a highly experienced otologist. Atresia patients who opt for surgery will temporarily have the canal packed with gelatin sponge and silicone sheeting to prevent closure. The timing of ear canal reconstruction (canalplasty) depends on the type of external ear (Microtia) repair desired by the patient and family. Two surgical teams in the USA are currently able to reconstruct the canal at the same time as the external ear in a single surgical stage (one stage ear reconstruction).

In cases where a later surgical reconstruction of the external ear of the child might be possible, positioning of the BAHA implant is critical. It may be necessary to position the implant further back than usual to enable successful reconstructive surgery – but not so far as to compromise hearing performance. If the reconstruction is ultimately successful, it is easy to remove the percutaneous BAHA abutment. If the surgery is unsuccessful, the abutment can be replaced and the implant re-activated to restore hearing.

Most of these conditions are self-correcting during childhood. In the worst cases, surgery may be needed. Most of the time, this involves lengthening the Achilles tendon. Less severe treatment options for pigeon toe include keeping a child from crossing his or her legs, use of corrective shoes, and casting of the foot and lower legs, which is normally done before the child reaches 12 months of age or older.

If the pigeon toe is mild and close to the center, treatment may not be necessary.

Ballet has been used as a treatment for mild cases. Dance exercises can help to bend the legs outward.

There is no clear form of treatment. Originally, bisphosphonates were expected to be of value after hip surgery but there has been no convincing evidence of benefit, despite having been used prophylactically.

Depending on the growth's location, orientation and severity, surgical removal may be possible.

Radiation Therapy.

Prophylactic radiation therapy for the prevention of heterotopic ossification has been employed since the 1970s. A variety of doses and techniques have been used. Generally, radiation therapy should be delivered as close as practical to the time of surgery. A dose of 7-8 Gray in a single fraction within 24–48 hours of surgery has been used successfully. Treatment volumes include the peri-articular region, and can be used for hip, knee, elbow, shoulder, jaw or in patients after spinal cord trauma.

Single dose radiation therapy is well tolerated and is cost effective, without an increase in bleeding, infection or wound healing disturbances.

Other possible treatments.

Certain antiinflammatory agents, such as indomethacin, ibuprofen and aspirin, have shown some effect in preventing recurrence of heterotopic ossification after total hip replacement.

Conservative treatments such as passive range of motion exercises or other mobilization techniques provided by physical therapists or occupational therapists may also assist in preventing HO. A review article looked at 114 adult patients retrospectively and suggested that the lower incidence of HO in patients with a very severe TBI may have been due to early intensive physical and occupational therapy in conjunction with pharmacological treatment. Another review article also recommended physiotherapy as an adjunct to pharmacological and medical treatments because passive range of motion exercises may maintain range at the joint and prevent secondary soft tissue contractures, which are often associated with joint immobility.

Congenital fourth cranial nerve palsy can be treated with strabismus surgery, where muscle attachment sites on the globe are modified to realign the eyes. Some eye doctors prefer conservative or no management of congenital fourth nerve palsy.

Other eye doctors recommend surgery early in a patient's life to prevent the compensatory torticollis and facial asymmetry that develop with age.

Prism lenses set to make minor optical changes in the vertical alignment may be prescribed instead of or after surgery to fine-tune the correction. Prism lenses do not address torsional misalignment and this may limit their use in certain cases. An additional consideration of prism lenses is that they must be worn at all times. Prism lenses reduce vertical fusional demands by allowing the eyes to rest in their vertically misaligned state. When they are removed the patient may experience vertical diplopia they find hard to resolve due to the rested state of their eyes.

Cases of congenital fourth nerve palsy vary in magnitude and way they affect the motion of the superior oblique muscle. Therefore different surgeries are available dependent upon the type of misalignment. Sometimes surgery on more than one eye muscle is required. In some simpler, unilateral cases a single surgery may suffice. In these cases the main problem is that the inferior oblique muscle of the same eye acts unopposed by the weakened superior oblique muscle, pulling the eye up. An example of a safe and effective procedure is a disinsertion of the inferior oblique muscle to allow it to reattach itself further down the globe of the eye. This acts to 'weaken' its action and allow the eye to move back into a more neutral alignment.

In all cases of congenital fourth nerve palsy, it is important to see an experienced strabismologist about management/treatment options. A strabismologist is an ophthalmologist (eye doctor) specialising in eye movement disorders.

Wearing shoes to protect barefoot trauma has shown decrease in incidence in ainhum. Congenital pseudoainhum cannot be prevented and can lead to serious birth defects.

Using the Ponseti method, the foot deformity is corrected in stages. These stages are as follows: manipulating the foot to an improved position and then holding it with a long leg cast, then removing the cast after a week, and then manipulating the foot again. The foot position usually improves over a course of 4-6 casts. The amount of casts varies from person to person to address each individual's characteristic needs.

- The initial cast focuses on aligning the forefoot with the hindfoot as Ponseti describes the forefoot as relatively pronated in comparison to the hindfoot. Supinating the forefoot and elevating the first metatarsal improves this alignment.

- Subsequent casts are applied after stretching the foot with a focus on abducting the forefoot with lateral pressure at the talus, to bring the navicula laterally and improve the alignment of the talonavicular joint. In contrast to the Kite Method of casting, it is important to avoid constraining the calcanocuboid joint. With each additional cast, the abduction is increased and this moves the hindfoot from varus into valgus. It is important to leave the ankle in equinus until the forefoot and hindfoot are corrected.

- The final stage of casting, is to correct the equinus. After fully abducting the forefoot with spontaneous correction of the hindfoot, an attempt is made to bring the ankle up and into dorsiflexion. For the majority of children, the equinus will not fully correct with casting and a procedure is done to facilitate this final aspect of the deformity correction. The procedure is a percutaneous heel cord release or Tenotomy. Ponseti advocated for doing this in the clinic with a local anesthetic. For safety reasons, many centers perform this procedure with sedation or monitored anesthesia care. In this procedure, numbing medicine is applied, the skin is cleansed, and a small scalpel is used to divide the Achilles tendon. With a small scalpel there is minimal bleeding and no need for stitches. A small dressing is applied and a final clubfoot cast is applied with the foot in a fully corrected position. This cast is typically left in place for 3 weeks.

After correction has been achieved with casting, maintenance of correction starts with full-time (23 hours per day) use of a brace —also known as a foot abduction brace (FAB)—on both feet, regardless of whether the TEV is on one side or both, typically full-time for 3 months. After 3 months, brace wear is decreased and used mostly when sleeping for naps and at night-time. This part-time bracing is recommended until the child is 4 years of age.

Roughly 30% of children will have recurrence. A recurrence can usually be managed with repeating the casting process. Recurrence is more common when there is poor compliance with the bracing, because the muscles around the foot can pull it back into the abnormal position. Approximately 20% of infants successfully treated with the Ponseti casting method will have an imbalance between the muscles that invert the ankle (posterior tibialis and anterior tibialis muscles) and the muscles that evert the ankle (peroneal muscles). Patients with this imbalance are more prone to recurrence. After 18 months of age, this can be addressed with surgery to transfer the anterior tibialis tendon from it medial attachment (the navicula) to a more lateral position (the lateral cuneiform) to rebalance these muscle forces. While this requires a general anesthetic and subsequent casting while the tendon heals, it is a relatively minor surgery that corrects a persistent muscle imbalance while avoiding disturbance to the joints of the foot.

The evidence for the use of medical interventions for lumbar spinal stenosis is poor. Injectable but not nasal calcitonin may be useful for short term pain relief. Epidural blocks may also transiently decrease pain, but there is no evidence of long-term effect. Adding steroids to these injections does not improve the result; the use of epidural steroid injections (ESIs) is controversial and evidence of their efficacy is contradictory.

Non-steroidal anti-inflammatory drugs (NSAIDs), muscle relaxants and opioid analgesics are often used to treat low back pain, but evidence of their efficacy is lacking.

Surgical treatment is only initiated if there is severe pain, as the available operations can be difficult. Otherwise, high arches may be handled with care and proper treatment.

Suggested conservative management of patients with painful pes cavus typically involves strategies to reduce and redistribute plantar pressure loading with the use of foot orthoses and specialised cushioned footwear. Other non-surgical rehabilitation approaches include stretching and strengthening of tight and weak muscles, debridement of plantar callosities, osseous mobilization, massage, chiropractic manipulation of the foot and ankle, and strategies to improve balance. There are also numerous surgical approaches described in the literature that are aimed at correcting the deformity and rebalancing the foot. Surgical procedures fall into three main groups:

1. soft-tissue procedures (e.g. plantar fascia release, Achilles tendon lengthening, tendon transfer);

2. osteotomy (e.g. metatarsal, midfoot or calcaneal);

3. bone-stabilising procedures (e.g. triple arthrodesis).

The prognosis is favorable in most patients with an isolated cutaneous abnormality. In the majority of cases, both the vivid red marking and the difference in circumference of the extremities regress spontaneously during the first year of life. It is theorized that this may be due to the normal maturation process, with thickening of the epidermis and dermis. Improvements for some patients can continue for up to 10 years, while in other cases, the marbled skin may persist for the patient's lifetime.

One study reported an improvement in lesions in 46% of patients within 3 years. If CMTC persists into adulthood, it can result in complaints due to paresthesia, increased sensitivity to cold and pain, and the formation of ulcers.

Few reports included long-term follow up of CMTC into adolescence and adulthood. While about 50% of patients seem to show definite improvement in the reticular vascular pattern, the exact incidence and cause of persistent cases are unknown.

Genetic counseling for VWS involves discussion of disease transmission in the autosomal dominant manner and possibilities for penetrance and expression in offspring. Autosomal dominance means affected parents have a 50% chance of passing on their mutated "IRF6" allele to a their child. Furthermore, if a cleft patient has lip pits, he or she has a ten times greater risk of having a child with cleft lip with or without cleft palate than a cleft patient who does not have lip pits. Types of clefting between parents and affected children are significantly associated; however, different types of clefts may occur horizontally and vertically within the same pedigree. In cases where clefting is the only symptom, a complete family history must be taken to ensure the patient does not have non-syndromic clefting.