Depending upon the treatment required, it is sometimes most appropriate to wait until later in life for a surgical remedy – the childhood growth of the face may highlight or increase the symptoms. When surgery is required, particularly when there is a severe disfiguration of the jaw, it is common to use a rib graft to help correct the shape.

According to literature, HFM patients can be treated with various treatment options such functional therapy with an appliance, distraction osteogenesis, or costochondral graft. The treatment is based on the type of severity for these patients. According to Pruzanksky's classification, if the patient has moderate to severe symptoms, then surgery is preferred. If patient has mild symptoms, then a functional appliance is generally used.

Patients can also benefit from a Bone Anchored Hearing Aid (BAHA).

While there is no cure for JBS, treatment and management of specific symptoms and features of the disorder are applied and can often be successful. Variability in the severity of JBS on a case-by-case basis determines the requirements and effectiveness of any treatment selected.

Pancreatic insufficiency and malabsorption can be managed with pancreatic enzyme replacement therapy, such as pancrelipase supplementation and other related methods.

Craniofacial and skeletal deformities may require surgical correction, using techniques including bone grafts and osteotomy procedures. Sensorineural hearing loss can be managed with the use of hearing aids and educational services designated for the hearing impaired.

Special education, specialized counseling methods and occupational therapy designed for those with mental retardation have proven to be effective, for both the patient and their families. This, too, is carefully considered for JBS patients.

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.

There is no treatment for the disorder. A number of studies are looking at gene therapy, exon skipping and CRISPR interference to offer hope for the future. Accurate determination through confirmed diagnosis of the genetic mutation that has occurred also offers potential approaches beyond gene replacement for a specific group, namely in the case of diagnosis of a so-called nonsense mutation, a mutation where a stop codon is produced by the changing of a single base in the DNA sequence. This results in premature termination of protein biosynthesis, resulting in a shortened and either functionless or function-impaired protein. In what is sometimes called "read-through therapy", translational skipping of the stop codon, resulting in a functional protein, can be induced by the introduction of specific substances. However, this approach is only conceivable in the case of narrowly circumscribed mutations, which cause differing diseases.

Prosthetic replacement of missing teeth is possible using dental implant technology or dentures. This treatment can be successful in giving patients with anodontia a more aesthetically pleasing appearance. The use of an implant prosthesis in the lower jaw could be recommended for younger patients as it is shown to significantly improve the craniofacial growth, social development and self-image. The study associated with this evidence worked with individuals who had ectodermal dysplasia of varying age groups of up to 11, 11 to 18 and more than 18 years. It was noted that the risk of implant failure was significantly higher in patients younger than 18 years, but there is significant reason to use this methodology of treatment in those older. Overall the use of an implant-prosthesis has a considerable functional, aesthetic and psychological advantage when compared to a conventional denture, in the patients.

Most patients suffering from KTS have epilepsy that is resistant to anti-epileptic agents. Some patients showed a partial response to treatment, but very few were able to stop their epilepsy through treatment. One case was responsive to treatment using Phenobartbital and vigabatrin which are both anti-epileptic agents. Spasticity can be treated with baclofen, but not all patients are responsive to the treatment.

Early intervention is considered important. For infants, breathing and feeding difficulties, are monitored. Therapies used are "symptomatic and supportive."

Camurati–Engelmann disease is somewhat treatable. Glucocorticosteroids, which are anti-inflammatory and immunosuppressive agents, are used in some cases. This form of medication helps in bone strength, however can have multiple side effects. In several reports, successful treatment with glucocoricosteroids was described, as certain side effects can benefit a person with CED. This drug helps with pain and fatigue as well as some correction of radiographic abnormalities.

Alternative treatments such as massage, relaxation techniques (meditation, essential oils, spa baths, music therapy, etc.), gentle stretching, and especially heat therapy have been successfully used to an extent in conjunction with pain medications. A majority of CED patients require some form of analgesics, muscle relaxant, and/or sleep inducing medication to manage the pain, specifically if experiencing frequent or severe 'flare-ups' (e.g. during winter).

Like treatment options, the prognosis is dependent on the severity of the symptoms. Despite the various symptoms and limitations, most individuals have normal intelligence and can lead a normal life.

A disease that threatens the eyesight and additionally produces a hair anomaly that is apparent to strangers causes harm beyond the physical. It is therefore not surprising that learning the diagnosis is a shock to the patient. This is as true of the affected children as of their parents and relatives. They are confronted with a statement that there are at present no treatment options. They probably have never felt so alone and abandoned in their lives. The question comes to mind, "Why me/my child?" However, there is always hope and especially for affected children, the first priority should be a happy childhood. Too many examinations and doctor appointments take up time and cannot practically solve the problem of a genetic mutation within a few months. It is therefore advisable for parents to treat their child with empathy, but to raise him or her to be independent and self-confident by the teenage years. Openness about the disease and talking with those affected about their experiences, even though its rarity makes it unlikely that others will be personally affected by it, will together assist in managing life.

Unerupted microdonts may require surgical removal to prevent the formation of cysts. Erupted microdonts, peg laterals especially, may cause cosmetic concern. Such teeth may be restored to resemble normal sized teeth, typically with composite build ups or crowns. Orthodontics may be required in severe cases to close gaps between the teeth.

Because kniest dysplasia can affect various body systems, treatments can vary between non-surgical and surgical treatment. Patients will be monitored over time, and treatments will be provided based on the complications that arise.

Because newborns can breathe only through their nose, the main goal of postnatal treatment is to establish a proper airway. Primary surgical treatment of FND can already be performed at the age of 6 months, but most surgeons wait for the children to reach the age of 6 to 8 years. This decision is made because then the neurocranium and orbits have developed to 90% of their eventual form. Furthermore, the dental placement in the jaw has been finalized around this age.

Autoimmune polyendocrine syndrome type 1 treatment is based on the symptoms that are presented by the affected individual, additionally there is:

- Hormone replacement

- Systemic antifungal treatment

- Immunosuppressive treatment

Structural nasal deformities are corrected during or shortly after the facial bipartition surgery. In this procedure, bone grafts are used to reconstruct the nasal bridge. However, a second procedure is often needed after the development of the nose has been finalized (at the age of 14 years or even later).

Secondary rhinoplasty is based mainly on a nasal augmentation, since it has been proven better to add tissue to the nose than to remove tissue. This is caused by the minimal capacity of contraction of the nasal skin after surgery.

In rhinoplasty, the use of autografts (tissue from the same person as the surgery is performed on) is preferred. However, this is often made impossible by the relative damage done by previous surgery. In those cases, bone tissue from the skull or the ribs is used. However, this may give rise to serious complications such as fractures, resorption of the bone, or a flattened nasofacial angle.

To prevent these complications, an implant made out of alloplastic material could be considered. Implants take less surgery time, are limitlessly available and may have more favorable characteristics than autografts. However, possible risks are rejection, infection, migration of the implant, or unpredictable changes in the physical appearance in the long term.

At the age of skeletal maturity, orthognathic surgery may be needed because of the often hypoplastic maxilla. Skeletal maturity is usually reached around the age of 13 to 16. Orthognathic surgery engages in diagnosing and treating disorders of the face and teeth- and jaw position.

The release of the first webspace has the same principle as the Snow-Littler procedure. The difference is the closure of the first webspace; this is done by simple closure or closure with Z-plasties.

Since Usher syndrome results from the loss of a gene, gene therapy that adds the proper protein back ("gene replacement") may alleviate it, provided the added protein becomes functional. Recent studies of mouse models have shown one form of the disease—that associated with a mutation in myosin VIIa—can be alleviated by replacing the mutant gene using a lentivirus. However, some of the mutated genes associated with Usher syndrome encode very large proteins—most notably, the "USH2A" and "GPR98" proteins, which have roughly 6000 amino-acid residues. Gene replacement therapy for such large proteins may be difficult.

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

The oral rehabilitation of hypodontia, especially where a significant number of teeth have not developed, is often a multidisciplinary process, involving a specialist orthodontist, a consultant in restorative dentistry, and a paediatric dentist in the earlier years. The process of treating and managing hypodontia begins in the early years of the patient's dentition where absent teeth are identified and the process of maintaining the remaining teeth begins. This is largely conducted by the paediatric dentist with orthodontic input. Once all the adult teeth have erupted the orthodontist is likely to liaise with the restorative dentist regarding optimal positioning of teeth for subsequent replacement with prosthodontic methods. This may include the utilisation of a resin-retained bridge and implants for spaces or composite resin, veneers or crowns where teeth are diminutive or misshaped.

Treatment of manifestations: special hair care products to help manage dry and sparse hair; wigs; artificial nails; emollients to relieve palmoplantar hyperkeratosis.

Bone marrow transplant may be possible for Severe Combined Immune Deficiency and other severe immunodeficiences.

Virus-specific T-Lymphocytes (VST) therapy is used for patients who have received hematopoietic stem cell transplantation that has proven to be unsuccessful. It is a treatment that has been effective in preventing and treating viral infections after HSCT. VST therapy uses active donor T-cells that are isolated from alloreactive T-cells which have proven immunity against one or more viruses. Such donor T-cells often cause acute graft-versus-host disease (GVHD), a subject of ongoing investigation. VSTs have been produced primarily by ex-vivo cultures and by the expansion of T-lymphocytes after stimulation with viral antigens. This is carried out by using donor-derived antigen-presenting cells. These new methods have reduced culture time to 10–12 days by using specific cytokines from adult donors or virus-naive cord blood. This treatment is far quicker and with a substantially higher success rate than the 3–6 months it takes to carry out HSCT on a patient diagnosed with a primary immunodeficiency. T-lymphocyte therapies are still in the experimental stage; few are even in clinical trials, none have been FDA approved, and availability in clinical practice may be years or even a decade or more away.

The treatment of primary immunodeficiencies depends foremost on the nature of the abnormality. Somatic treatment of primarily genetic defects is in its infancy. Most treatment is therefore passive and palliative, and falls into two modalities: managing infections and boosting the immune system.

Reduction of exposure to pathogens may be recommended, and in many situations prophylactic antibiotics or antivirals may be advised.

In the case of humoral immune deficiency, immunoglobulin replacement therapy in the form of intravenous immunoglobulin (IVIG) or subcutaneous immunoglobulin (SCIG) may be available.

In cases of autoimmune disorders, immunosuppression therapies like corticosteroids may be prescribed.

The surgery to correct hypertelorism is usually done between 5 and 8 years of age. This addresses the psychosocial aspects in the child's early school years. Another reason for correction age 5 or older is that the surgery should be delayed until the tooth buds have grown out low enough into the maxilla, thus preventing damage to them. Also, before age 5 the craniofacial bones are thin and fragile, which can make surgical correction difficult. In addition, it is possible that orbital surgery during infancy may inhibit midface growth.

For the treatment of hypertelorism there are 2 main operative options: The box osteotomy and the facial bipartition (also referred to as median fasciotomy).

Webbed toes can be separated through surgery. Surgical separation of webbed toes is an example of body modification.

As with any form of surgery, there are risks of complications.

The end results depend on the extent of the webbing and underlying bone structure. There is usually some degree of scarring, and skin grafts may be required. In rare instances, nerve damage may lead to loss of feeling in the toes and a tingling sensation. There are also reports of partial web grow-back. The skin grafts needed to fill in the space between the toes can lead to additional scars in the places where the skin is removed.

MRI will help with the diagnosis of structural abnormality of the brain. Genetic testing may also be pursued.