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.

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).

Surgical treatment of the cleft hand is based on several indications:

Improving function

- Absent thumb

- Deforming syndactyly (mostly between digits of unequal length like index and thumb)

- Transverse bones (this will progress the deformity; growth of these bones will widen the cleft)

- Narrowed first webspace

- The feet

Aesthetical aspects

- Reducing deformity

The treatment of individuals with TCS may involve the intervention of professionals from multiple disciplines. The primary concerns are breathing and feeding, as a consequence of the hypoplasia of the mandibula and the obstruction of the hypopharynx by the tongue. Sometimes, they may require a tracheostomy to maintain an adequate airway, and a gastrostomy to assure an adequate caloric intake while protecting the airway. Corrective surgery of the face is performed at defined ages, depending on the developmental state.

An overview of the present guidelines:

- If a cleft palate is present, the repair normally takes place at 9–12 months old. Before surgery, a polysomnography with a palatal plate in place is needed. This may predict the postoperative situation and gives insight on the chance of the presence of sleep apnea (OSAS) after the operation.

- Hearing loss is treated by bone conduction amplification, speech therapy, and educational intervention to avoid language/speech problems. The bone-anchored hearing aid is an alternative for individuals with ear anomalies

- Zygomatic and orbital reconstruction is performed when the cranio-orbitozygomatic bone is completely developed, usually at the age of 5–7 years. In children, an autologous bone graft is mostly used. In combination with this transplantation, lipofilling can be used in the periorbital area to get an optimal result of the reconstruction. Reconstruction of the lower eyelid coloboma includes the use of a myocutaneous flap, which is elevated and in this manner closes the eyelid defect.

- External ear reconstruction is usually done when the individual is at least eight years old. Sometimes, the external auditory canal or middle ear can also be treated.

- The optimal age for the maxillomandibular reconstruction is controversial; as of 2004, this classification has been used:

1. Type I (mild) and Type IIa (moderate) 13–16 years

2. Type IIb (moderate to severe malformation) at skeletal maturity

3. Type III (severe) 6–10 years

- When the teeth are cutting, the teeth should be under supervision of an orthodontist to make sure no abnormalities occur. If abnormalities like dislocation or an overgrowth of teeth are seen, appropriate action can be undertaken as soon as possible.

- Orthognatic treatments usually take place after the age of 16 years; at this point, all teeth are in place and the jaw and dentures are mature. Whenever OSAS is detected, the level of obstruction is determined through endoscopy of the upper airways. Mandibular advancement can be an effective way to improve both breathing and æsthetics, while a chinplasty only restores the profile.

- If a nose reconstruction is necessary, it is usually performed after the orthognatic surgery and after the age of 18 years.

- The contour of the facial soft tissues generally requires correction at a later age, because of the facial skeletal maturity. The use of microsurgical methods, like the free flap transfer, has improved the correction of facial soft tissue contours. Another technique to improve the facial soft tissue contours is lipofilling. For instance, lipofilling is used to reconstruct the eyelids.

There is no single course of medical treatment or cure for Möbius syndrome. Treatment is supportive and in accordance with symptoms. If they have difficulty nursing, infants may require feeding tubes or special bottles to maintain sufficient nutrition. Physical, occupational, and speech therapy can improve motor skills and coordination and can lead to better control of speaking and eating abilities. Often, frequent lubrication with eye drops is sufficient to combat dry eye that results from impaired blinking. Surgery can correct crossed eyes, protect the cornea via tarsorraphy, and improve limb and jaw deformities. Sometimes called smile surgery by the media, muscle transfers grafted from the thigh to the corners of the mouth can be performed to provide the ability to smile. Although "smile surgery" may provide the ability to smile, the procedure is complex and can take twelve hours for each side of the face. Also, the surgery cannot be considered a "cure" for Möbius syndrome, because it does not improve the ability to form other facial expressions.

While Larsen syndrome can be lethal if untreated, the prognosis is relatively good if individuals are treated with orthopedic surgery, physical therapy, and other procedures used to treat the symptoms linked with Larsen syndrome.

Treatment is usually confined to such surgical intervention as may be necessary to help the child to develop e.g. jaw distraction/bone grafts, ocular dermoid debulking (see below), repairing cleft palate/lip, repairing heart malformations or spinal surgery. Some patients with Goldenhar syndrome will require assistance as they grow by means of hearing aids or glasses.

Stem cell grafting (womb tissue grafting) has been successfully used to "reprogram" eye dermoids, effectively halting the regrowth of eye dermoids.

These tissues that grow on the eye are "mis-programmed" cells (sometimes tooth or nail cells instead of eye cells).

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.

Treatment for Larsen syndrome varies according to the symptoms of the individual. Orthopedic surgery can be performed to correct the serious joint defects associated with Larsen syndrome. Reconstructive surgery can be used to treat the facial abnormalities. Cervical kyphosis can be very dangerous to an individual because it can cause the vertebrae to disturb the spinal cord. Posterior cervical arthrodesis has been performed on patients with cervical kyphosis, and the results have been successful Propranolol has been used to treat some of the cardiac defects associated with Marfan's syndrome, so the drug also has been suggested to treat cardiac defects associated with Larsen syndrome.

There are several options for treatment of mouth anomalies like Tessier cleft number 2-3-7 . These clefts are also seen in various syndromes like Treacher Collins syndrome and hemifacial microsomia, which makes the treatment much more complicated. In this case, treatment of mouth anomalies is a part of the treatment of the syndrome.

The goals of treatment in infants with Robin sequence focus upon breathing and feeding, and optimizing growth and nutrition despite the predisposition for breathing difficulties. If there is evidence of airway obstruction (snorty breathing, apnea, difficulty taking a breath, or drops in oxygen), then the infant should be placed in the sidelying or prone position, which helps bring the tongue base forward in many children. One study of 60 infants with PRS found that 63% of infants responded to prone positioning (Smith and Senders, 2006, Int J Pediatr Oto). 53% of the infants in this study required some form of feeding assistance, either nasogastric tube or gastrostomy tube feedings (feeding directly into the stomach). In a separate study of 115 children with the clinical diagnosis of PRS managed at 2 different hospitals in Boston (Evans et al., 2006, In J Pediatr Oto), respiratory distress was managed successfully in 56% without an operation (either by prone positioning, short term intubation, or placement of a nasopharyngeal airway). In this study, gastrostomy tube feeding were placed in 42% of these infants due to feeding difficulties.

Gastroesophageal reflux (GERD) seems to be more prevalent in children with Robin sequence (Dudkiewicz, March 2000, CPCJ). Because reflux of acidic contents in the posterior pharynx and upper airway can intensify the symptoms of Robin sequence, specifically by worsening airway obstruction, it is important to maximize treatment for GER in children with PRS and reflux symptoms. Treatment may include upright positioning on a wedge (a tucker sling may be needed if the baby is in the prone position), small and frequent feedings (to minimize vomiting), and/or pharmacotherapy (such as proton pump inhibitors).

In nasopharyngeal cannulation (or placement of the nasopharyngeal airway or tube), the infant is fitted with a blunt-tipped length of surgical tubing (or an endotracheal tube fitted to the child), which is placed under direct visualization with a laryngoscope, being inserted into the nose and down the pharynx (or throat), ending just above the vocal cords. Surgical threads fitted through holes in the outside end of the tube are attached to the cheek with a special skin-like adhesive material called 'stomahesive', which is also wrapped around the outside end of the tube (but not over the opening at the end) to keep the tube in place. This tube or cannula, which itself acts as an airway, primarily acts as a sort of "splint" which maintains patency of the airway by keeping the tongue form falling back on the posterior pharyngeal wall and occluding the airway, therefore preventing airway obstruction, hypoxia and asphyxia. Nasopharyngeal airways are not available at every center, however, when available, nasopharyngeal cannulation should be favored over the other treatments mentioned in this article, as it is far less invasive; it allows the infant to feed without the further placement of a nasogastric tube. This treatment may be utilized for multiple months, until the jaw has grown enough so that the tongue assumes a more normal position in the mouth and airway (at birth, the jaws of some infants are so underdeveloped that only the tip of the tongue can be seen when viewed in the throat). Some institutions discharge the infant home with a nasopharyngeal tube in place (Citation: KD Anderson, May 2007, CPCJ).

Distraction osteogenesis (DO), also called a "Mandibular Distraction", can be used to correct abnormal smallness of one or both jaws seen in patients with Robin Sequence. Enlargement of the lower jaw brings the tongue forward, preventing it from obstructing the upper airway. The process of DO begins with preoperative assessment. Doctors use three-dimensional imaging to identify the parts of the patient's facial skeleton that need repositioning and determine the magnitude and direction of distraction. They may then select the most appropriate distraction device or sometimes have custom devises fabricated. When possible, intraoral devices are used.

DO surgery starts with an osteotomy (surgical division or sectioning of bone) followed by the distraction device being placed under the skin and across the osteotomy. A few days later, the two ends of the bone are very gradually pulled apart through continual adjustments that are made to the device by the parents at home. The adjustments are made by turning a small screw that protrudes through the skin, usually at a rate of 1 mm per day. This gradual distraction leads to formation of new bone between the two ends. After the process is complete, the osteotomy is allowed to heal over a period of six to eight weeks. A small second surgery is then performed to remove the device.

The cleft palate is generally repaired between the ages of 6½ months and 2 years by a plastic or maxillofacial surgeon. In many centres there is now a cleft lip and palate team comprising both of these specialties, as well as a coordinator, a speech and language therapist, an orthodontist, sometimes a psychologist or other mental health specialist, an audiologist, an otorhinolaryngologist (ENT surgeon) and nursing staff. The glossoptosis and micrognathism generally do not require surgery, as they improve to some extent unaided, though the mandibular arch remains significantly smaller than average. In some cases jaw distraction is needed to aid in breathing and feeding. Lip-tongue attachment is performed in some centres, though its efficacy has been recently questioned.

Cleft lip and palate is very treatable; however, the kind of treatment depends on the type and severity of the cleft.

Most children with a form of clefting are monitored by a "cleft palate team" or "craniofacial team" through young adulthood. Care can be lifelong. Treatment procedures can vary between craniofacial teams. For example, some teams wait on jaw correction until the child is aged 10 to 12 (argument: growth is less influential as deciduous teeth are replaced by permanent teeth, thus saving the child from repeated corrective surgeries), while other teams correct the jaw earlier (argument: less speech therapy is needed than at a later age when speech therapy becomes harder). Within teams, treatment can differ between individual cases depending on the type and severity of the cleft.

There is no cure as of now. Treatment is directed towards the specific symptoms that are present in each individual. Individuals with hearing loss are able to get treated with hearing aids.

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.

A craniofacial team is routinely used to treat this condition. The majority of hospitals still use craniofacial teams; yet others are making a shift towards dedicated cleft lip and palate programs. While craniofacial teams are widely knowledgeable about all aspects of craniofacial conditions, dedicated cleft lip and palate teams are able to dedicate many of their efforts to being on the cutting edge of new advances in cleft lip and palate care.

Many of the top pediatric hospitals are developing their own CLP clinics in order to provide patients with comprehensive multi-disciplinary care from birth through adolescence. Allowing an entire team to care for a child throughout their cleft lip and palate treatment (which is ongoing) allows for the best outcomes in every aspect of a child's care. While the individual approach can yield significant results, current trends indicate that team based care leads to better outcomes for CLP patients. .

The only treatment for MWS is only symptomatic, with multidisciplinary management

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.

There is no single strategy for treatment of facial clefts, because of the large amount of variation in these clefts. Which kind of surgery is used depends on the type of clefting and which structures are involved. There is much discussion about the timing of reconstruction of bone and soft tissue. The problem with early reconstruction is the recurrence of the deformity due to the intrinsic restricted growth. This requires additional operations at a later age to make sure all parts of the face are in proportion. A disadvantage of early bone reconstruction is the chance to damage the tooth germs, which are located in the maxilla, just under the orbit. The soft tissue reconstruction can be done at an early age, but only if the used skin flap can be used again during a second operation. The timing of the operation depends on the urgency of the underlying condition. If the operation is necessary to function properly, it should be done at early age. The best aesthetic result is achieved when the incisions are positioned in areas which attract the least attention (they cover up the scars). If, however, the function of a part of the face isn’t damaged, the operation depends on psychological factors and the facial area of reconstruction.

The treatment plan of a facial cleft is planned right after diagnosis. This plan includes every operation needed in the first 18 years of the patients life to reconstruct the face fully.

In this plan, a difference is made between problems that need to be solved to improve the health of the patient (coloboma) and problems that need to be solved for a better cosmetic result (hypertelorism).

The treatment of the facial clefts can be divided in different areas of the face: the cranial anomalies, the orbital and eye anomalies, the nose anomalies, the midface anomalies and the mouth anomalies.

There is no known curative treatment presently. Hearing aids and cataract surgery may be of use. Control of seizures, heart failure and treatment of infection is important. Tube feeding may be needed.

The disorder can be associated with a number of psychological symptoms, anxiety, depression, social phobia, body image disorders, and patients may be subjected to discrimination, bullying and name calling especially when young. A multi-disciplinary team and parental support should include these issues.

There is no medical treatment for either syndrome but there are some recommendations that can help with prevention or early identification of some of the problems. Children with either syndrome should have their hearing tested, and adults should be aware that the hearing loss may not develop until the adult years. Yearly visits to an ophthalmologist or other eye care professional who has been informed of the diagnosis of Stickler or Marshall syndrome is important for all affected individuals. Children should have the opportunity to have myopia corrected as early as possible, and treatment for cataracts or detached retinas may be more effective with early identification. Support for the joints is especially important during sports, and some recommend that contact sports should be avoided by those who have very loose joints.

Many of the congenital malformations found with Malpuech syndrome can be corrected surgically. These include cleft lip and palate, omphalocele, urogenital and craniofacial abnormalities, skeletal deformities such as a caudal appendage or scoliosis, and hernias of the umbillicus. The primary area of concern for these procedures applied to a neonate with congenital disorders including Malpuech syndrome regards the logistics of anesthesia. Methods like tracheal intubation for management of the airway during general anesthesia can be hampered by the even smaller, or maldeveloped mouth of the infant. For regional anesthesia, methods like spinal blocking are more difficult where scoliosis is present. In a 2010 report by Kiernan et al., a four-year-old girl with Malpuech syndrome was being prepared for an unrelated tonsillectomy and adenoidectomy. While undergoing intubation, insertion of a laryngoscope, needed to identify the airway for the placement of the endotracheal tube, was made troublesome by the presence of micrognathia attributed to the syndrome. After replacement with a laryngoscope of adjusted size, intubation proceeded normally. Successful general anesthesia followed.

A rare follow-up of a male with Malpuech syndrome was presented by Priolo et al. (2007). Born at term from an uneventful pregnancy and delivery, the infant underwent a surgical repair of a cleft lip and palate. No problems were reported with the procedure. A heart abnormality, atrial septal defect, was also apparent but required no intervention. At age three years, mental retardation, hyperactivity and obsessive compulsive disorder were diagnosed; hearing impairment was diagnosed at age six, managed with the use of hearing aids. Over the course of the decade that followed, a number of psychiatric evaluations were performed. At age 14, he exhibited a fear of physical contact; at age 15, he experienced a severe psychotic episode, characterized by agitation and a loss of sociosexual inhibition. This array of symptoms were treated pharmocologically (with prescription medications). He maintained a low level of mental deficiency by age 17, with moments of compulsive echolalia.

Treatment of Roberts syndrome is individualized and specifically aimed at improving the quality of life for those afflicted with the disorder. Some of the possible treatments include: surgery for the cleft lip and palate, correction of limb abnormalities (also through surgery), and improvement in prehensile hand grasp development.

Children affected with PRS usually reach full development and size. However, it has been found internationally that children with PRS are often slightly below average size, raising concerns of incomplete development due to chronic hypoxia related to upper airway obstruction as well as lack of nutrition due to early feeding difficulties or the development of an oral aversion. However, the general prognosis is quite good once the initial breathing and feeding difficulties are overcome in infancy. Most PRS babies grow to lead a healthy and normal adult life.

The most important medical problems are difficulties in breathing and feeding. Affected infants very often need assistance with feeding, for example needing to stay in a lateral(on the side) or prone(on the tummy) position which helps bring the tongue forward and opens up the airway. Babies with a cleft palate will need a special cleft feeding device (such as the Haberman Feeder). Infants who are unable to take in enough calories by mouth to ensure growth may need supplementation with a nasogastric tube. This is related to the difficulty in forming a vacuum in the oral cavity related to the cleft palate, as well as to breathing difficulty related to the posterior position of the tongue. Given the breathing difficulties that some babies with PRS face, they may require more calories to grow (as working of breathing is somewhat like exercising for an infant). Infants, when moderately to severely affected, may occasionally need nasopharyngeal cannulation, or placement of a nasopharyngeal tube to bypass the airway obstruction at the base of the tongue. in some places, children are discharged home with a nasopharyngeal tube for a period of time, and parents are taught how to maintain the tube. Sometimes endotracheal intubation or tracheostomy may be indicated to overcome upper respiratory obstruction. In some centers, a tongue lip adhesion is performed to bring the tongue forward, effectively opening up the airway. Mandibular distraction can be effective by moving the jaw forward to overcome the upper airway obstruction caused by the posterior positioning of the tongue.

Given that a proportion of children with Robin sequence will have Stickler syndrome, it is important that a child with PRS have an evaluation by an optometrist or ophthalmologist in the first year of life looking for myopia that can be seen in Stickler syndrome. Because retinal detachment that can occur in Stickler syndrome is a leading cause of blindness in children, it is very important to recognize and be thoughtful of this diagnosis.

Similar to all genetic diseases Aarskog–Scott syndrome cannot be cured, although numerous treatments exist to increase the quality of life.

Surgery may be required to correct some of the anomalies, and orthodontic treatment may be used to correct some of the facial abnormalities. Trials of growth hormone have been effective to treat short stature in this disorder.