Patients must have early consultation with craniofacial and orthopaedic surgeons, when craniofacial, clubfoot, or hand correction is indicated to improve function or aesthetics. Operative measures should be pursued cautiously, with avoidance of radical measures and careful consideration of the abnormal muscle physiology in Freeman–Sheldon syndrome. Unfortunately, many surgical procedures have suboptimal outcomes, secondary to the myopathy of the syndrome.

When operative measures are to be undertaken, they should be planned for as early in life as is feasible, in consideration of the tendency for fragile health. Early interventions hold the possibility to minimise developmental delays and negate the necessity of relearning basic functions.

Due to the abnormal muscle physiology in Freeman–Sheldon syndrome, therapeutic measures may have unfavourable outcomes. Difficult endotracheal intubations and vein access complicate operative decisions in many DA2A patients, and malignant hyperthermia (MH) may affect individuals with FSS, as well. Cruickshanks et al. (1999) reports uneventful use of non-MH-triggering agents. Reports have been published about spina bifida occulta in anaesthesia management and cervical kyphoscoliosis in intubations.

Emanuel Syndrome does not have a cure, but individual symptoms may be treated. Assessments of individual systems, such as the cardiovascular, gastrointestinal, orthopedic, and neurological may be necessary to determine the extent of impairment and options for treatment.

Patients and their parents must receive psychotherapy, which should include marriage counselling. Mitigation of lasting psychological problems, including depression secondary to chronic illness and posttraumatic stress disorder (PTSD), can be very successfully addressed with early interventions. This care may come from the family physician, or other attending physician, whoever is more appropriate; specialist care is generally not required. Lewis and Vitulano (2003) note several studies suggesting predisposal for psychopathology in paediatric patients with chronic illness. Esch (2002) advocates preventive psychiatry supports to facilitate balance of positive and negative stressors associated with chronic physical pathology. Patients with FSS should have pre-emptive and ongoing mixed cognitive therapy-psychodynamic psychotherapy for patients with FSS and cognitive-behavioural therapy (CBT), if begun after onset of obvious pathology.

Adler (1995) cautioned the failure of modern medicine to implement the biopsychosocial model, which incorporates all aspects of a patient’s experience in a scientific approach into the clinical picture, often results in chronically-ill patients deferring to non-traditional and alternative forms of therapy, seeking to be understood as a whole, not a part, which may be problematic among patients with FSS.

Furthermore, neuropsychiatry, physiological, and imaging studies have shown PTSD and depression to be physical syndromes, in many respects, as they are psychiatric ones in demonstrating limbic system physiological and anatomy disturbances. Attendant PTSD hyperarousal symptoms, which additionally increase physiological stress, may play a part in leading to frequent MH-like hyperpyrexia and speculate on its influence on underlying myopathology of FSS in other ways. PTSD may also bring about developmental delays or developmental stagnation, especially in paediatric patients.

With psychodynamic psychotherapy, psychopharmacotherapy may need to be considered. Electroconvulsive therapy (ECT) is advised against, in light of abnormal myophysiology, with predisposal to MH.

Children with CHARGE syndrome may have a number of life-threatening medical conditions; with advances in medical care, these children can survive and can thrive with the support of a multidisciplinary team of medical professionals. Therapies and education must take into consideration hearing impairment, vision problems, and any others. Early intervention, such as occupational, speech-language, and physical therapy, to improve static posture, ambulation, and self-care skills is important. The intelligence of children with multiple health impairments, such as combined deafblindness, can be underestimated in the absence of early intervention.

There are no treatment to return to its normal functions. However, there are treatments for the different symptoms.

For the Developmental symptoms, Educational intervention and speech therapy beginning in infancy could help to reduce the high risk for motor, cognitive, speech, and language delay

For theSkeletal features, referral to an orthopedist for consideration of surgical release of contractures. In addition,early referral to physical therapy could help increase joint mobility.

Lastly, Thyroid hormone replacement could help out the thyroid dysfunction

Treatment of 3-M syndrome is aimed at the specific symptoms presented in each individual. With the various symptoms of this disorder being properly managed and affected individuals having normal mental development, 3-M syndrome is not a life - threatening condition and individuals are able to lead a near normal life with normal life expectancy.

Treatment may involve the coordinated efforts of many healthcare professionals, such as pediatricians, orthopedists, dentists and/or other specialists depending on the symptoms.

- Possible management options for short stature are surgical bone lengthening or growth hormone therapy.

- Orthopedic techniques and surgery may be used to treat certain skeletal abnormalities.

- Plastic surgery may also be performed on individuals to help correct certain cranio-facial anomalies.

- Individuals with dental abnormalities may undergo corrective procedures such as braces or oral surgeries.

Children with CHARGE syndrome will vary greatly in their abilities in the classroom: some may need little support, while some may require full-time support and individualized programs.

Taking each of the various affected body systems into account is vital to the success of the child in the educational setting.

An important step in dealing with abnormal behavior is understanding why it is occurring and helping the child learn more appropriate methods of communicating. Before a child reaches age 18 (or the age of maturity in their country) doctors and specialists need to be found that will follow the individual in adulthood.

Each child is different and it entirely depends on which sutures are fused and how it is affecting the child as to how it is treated. Some children have severe breathing issues due to shallow mid face and may require a tracheostomy. All should be treated at a specialist centre. Cranio bands are not used in the UK.

Surgery is typically used to prevent the closure of sutures of the skull from damaging the brain's development. Without surgery, blindness and mental retardation are typical outcomes. Craniofacial surgery is a discipline of both plastic surgery and oral and maxillofacial surgery (OMFS) . To move the orbits forward, craniofacial surgeons expose the skull and orbits and reshape the bone. To treat the midface deficiency, craniofacial surgeons can move the lower orbit and midface bones forward. For jaw surgery, either plastic surgeons or OMFS surgeons can perform these operations.

Crouzon patients tend to have multiple sutures involved, most specifically bilateral coronal craniosynostoses, and either open vault surgery or strip craniectomy (if child is under 6 months) can be performed. In the later scenario, a helmet is worn for several months following surgery.

Once treated for the cranial vault symptoms, Crouzon patients generally go on to live a normal lifespan.

Treatment for CLSD is largely focused on treating the symptoms of the disorder, because it is still in the early stages of research. Symptomatic treatment is also the only option due to the genetic nature of the disorder. Treatment may include surgeries to correct facial and cranial dysmorphisms or therapy sessions to help alleviate behavioral abnormalities associated with the disorder.

Though the children affected with CLSD will have problems throughout life, the treatment for this disease thus far is symptomatic. However, prognosis is good; at the time of the most recently published articles, identified children were still alive at over 4 years of age.

Mutant proteins still maintain some residual activity, allowing for the release of some collagen, but still form an extremely distended endoplasmic reticulum.

Recent research has been focused on studying large series of cases of 3-M syndrome to allow scientists to obtain more information behind the genes involved in the development of this disorder. Knowing more about the underlying mechanism can reveal new possibilities for treatment and prevention of genetic disorders like 3-M syndrome.

- One study looks at 33 cases of 3M syndrome, 23 of these cases were identified as CUL7 mutations: 12 being homozygotes and 11 being heterozygotes. This new research shows genetic heterogeneity in 3M syndrome, in contrast to the clinical homogeneity. Additional studies are still ongoing and will lead to the understanding of this new information.

- This study provides more insight on the three genes involved in 3M syndrome and how they interact with each other in normal development. It lead to the discovery that the CUL7, OBS1, and CCDC8 form a complex that functions to maintain microtubule and genomic integrity.

Children with WAGR syndrome receive regular (3-4 yearly) kidney surveillance for Wilms' tumour until at least the age of 6–8 years and thereafter remain under some follow-up because of the risk of late onset nephropathy (40% of patients over the age of 12 years). Females with WAGR syndrome may have streak ovaries, which can increase the risk for gonadoblastoma. Malformations of the vagina and/or uterus may also be present.

The most obvious, and often important part of treatment, is avoiding exposure to sunlight. This includes wearing protective clothing and using sunscreen (physical and chemical). Keratosis can also be treated using cryotherapy or fluorouracil. Theoretically, the condition could be completely corrected if functionally intact (non-mutated) endonuclease genes could be inserted into every cell into the body, and the most promising method to do this would be crispr. However, every cell in the body would have to be penetrated for a total cure, because the skin does not protect against other forms of radiation, like x-rays, even at low quantities harmless for those without xeroderma pigmentosa.

Donnai–Barrow syndrome is a genetic disorder first described by Dian Donnai and Margaret Barrow in 1993. It is associated with "LRP2". It is an inherited (genetic) disorder that affects many parts of the body.

Urban–Rogers–Meyer syndrome, also known as Prader–Willi habitus, osteopenia, and camptodactyly or Urban syndrome, is an extremely rare inherited congenital disorder first described by Urban et al. (1979). It is characterized by genital anomalies, mental retardation, obesity, contractures of fingers, and osteoporosis, though further complications are known.

McKusick–Kaufman syndrome is a genetic condition associated with MKKS.

The condition is named for Dr. Robert L. Kaufman and Victor McKusick. It is sometimes known by the abbreviation MKS. In infancy it can be difficult to distinguish between MKS and the related Bardet–Biedl syndrome, as the more severe symptoms of the latter condition rarely materialise before adulthood.

XX males are sterile due to low or no sperm content and there is currently no treatment to address this infertility. Genital ambiguities, while not necessary to treat for medical reasons, can be treated through the use of hormonal therapy, surgery, or both. Since XX male syndrome is variable in its presentation, the specifics of treatment varies widely as well. In some cases gonadal surgery can be performed to remove partial or whole female genitalia. This may be followed by plastic and reconstructive surgery to make the individual appear more externally male. Conversely, the individual may wish to become more feminine and feminizing genitoplasty can be performed to make the ambiguous genitalia appear more female. Hormonal therapy may also aid in making an individual appear more male or female.

Derivative 22 syndrome, or der(22), is a rare disorder associated with multiple congenital anomalies, including profound mental retardation, preauricular skin tags or pits, and conotruncal heart defects. It can occur in offspring of carriers of the constitutional chromosomal translocation t(11;22)(q23;q11), owing to a 3:1 meiotic malsegregation event resulting in partial trisomy of chromosomes 11 and 22. An unbalanced translocation between chromosomes 11 & 22 is described as Emanuel syndrome. It was characterized in 1980.

Young–Madders syndrome, alternatively known as Pseudotrisomy 13 syndrome or holoprosencephaly–polydactyly syndrome, is a genetic disorder resulting from defective and duplicated chromosomes which result in holoprosencephaly, polydactyly, facial malformations and mental retardation, with a significant variance in the severity of symptoms being seen across known cases. Many cases often suffer with several other genetic disorders, and some have presented with hypoplasia, cleft lip, cardiac lesions and other heart defects. In one case in 1991 and another in 2000 the condition was found in siblings who were the product of incest. Many cases are diagnosed prenatally and often in siblings. Cases are almost fatal in the prenatal stage with babies being stillborn.

Though it is now thought that earlier cases were misdiagnosed as other genetic disorders with similar pathology—such as Smith–Lemli–Opitz syndrome—the earliest publicised recognition of the condition as a new, hitherto unclassified, genetic disorder was made by two British doctors in Leicester in 1987. Though they identified the condition, later named for them, they did not identify the genetic anomalies responsible but suspected a link with trisomy 13 due to the similar symptoms. With only one or two occurrences documented towards the end of the decade, a group of eight doctors published a five-patient case-study in 1991 which identified the likely chromosomal factors that caused the condition, similar to but distinct from trisomy 13, and gave it the name 'holoprosencephaly–polydactyly syndrome' based on its two most prolific presenting conditions. Later research showed that the condition could manifest in patients with normal karyotypes, without duplication of the chromosomes, and the most recent genetic research implicates problems with the gene code FBXW11 as a likely cause.

Seaver Cassidy syndrome is a very rare disorder characterized by certain facial, genital, and skeletal deformities, as well as an unusual susceptibility to bleeding. Seaver Cassidy syndrome was first described in 1991 by Laurie Seaver and Suzanne Cassidy.

Clinically, McKusick–Kaufman syndrome is characterized by a combination of three features: postaxial polydactyly, heart defects, and genital abnormalities:

- Vaginal atresia with hydrometrocolpos

- Double vagina and/or uterus.

- Hypospadias, chordee (a downward-curving penis), and undescended testes (cryptorchidism).

- ureter stenosis or ureteric atresia

Young's syndrome, also known as azoospermia sinopulmonary infections, sinusitis-infertility syndrome and Barry-Perkins-Young syndrome, is a rare condition that encompasses a combination of syndromes such as bronchiectasis, rhinosinusitis and reduced fertility. In individuals with this syndrome, the functioning of the lungs is usually normal but the mucus is abnormally viscous. The reduced fertility (azoospermia) is due to functional obstruction of sperm transport down the genital tract at the epididymis where the sperms are found in viscous, lipid-rich fluid. The syndrome was named after Donald Young, the urologist who first made observations of the clinical signs of the syndrome in 1972. There have been several studies undertaken suggesting that contact with mercury might cause the syndrome.

A variant of Young's syndrome has been observed in an individual, showing slightly different signs and symptoms.

Signs of Seaver Cassidy syndrome include several facial disorders, including hypertelorism and telecanthus, epicanthal folds, downslanting palpebral fissures, ptosis, a broad nasal bridge, malar hypoplasia, a thin upper lip, a smooth philtrum, and low-set, prominent ears. Males with Seaver Cassidy syndrome may also experience an underdeveloped shawl scrotum and cryptorchidism. Skeletal anomalies, such genu valgum, hyperextended joints, or cubitus valgus, may also be present.

Young–Madders syndrome is detectable from the fetal stage of development largely due to the distinctive consequences of holoprosencephaly, a spectrum of defects or malformations of the brain and face. Facial defects which may manifest in the eyes, nose, and upper lip, featuring cyclopia, anosmia, or in the growth of only a single central incisor, and severe overlapping of the bones of the skull. Cardiac and in some cases pulmonary deformities are present. Another signature deformity is bilateral polydactyly, and many patients also suffer from hypoplasia and genital deformities.

Genitopatellar syndrome is a rare disorder with characteristic craniofacial features, congenital flexion contractures of the lower limbs, absent or abnormal patellae, urogenital anomalies, and severe psychomotor retardation.

In 2012, it was shown that mutations in the gene KAT6B cause the syndrome.