Colobomas of the iris may be treated in a number of ways. A simple cosmetic solution is a specialized cosmetic contact lens with an artificial pupil aperture. Surgical repair of the iris defect is also possible. Surgeons can close the defect by stitching in some cases. More recently artificial iris prosthetic devices such as the Human Optics artificial iris have been used successfully by specialist surgeons. This device cannot be used if the natural lens is in place and is not suitable for children. Suture repair is a better option where the lens is still present.

Vision can be improved with glasses, contact lenses or even laser eye surgery but may be limited if the retina is affected or there is amblyopia.

A 2009 study, widely reported in the popular press, has suggested that repetitive transcranial magnetic stimulation may temporarily improve contrast sensitivity and spatial resolution in the affected eye of adults with amblyopia. This approach is still under development, and the results await verification by other researchers. It has also been suggested that comparable results can be achieved using different types of brain stimulation such as anodal transcranial direct current stimulation and theta burst rTMS.

A 2013 study concluded that converging evidence indicates decorrelated binocular experience plays a pivotal role in the genesis of amblyopia and the associated residual deficits. Another study of 2013 suggests that playing a version of the popular game Tetris that is modified such that each eye sees separate components of the game may also help to treat this condition in adults. Furthermore, it has been proposed that the effects of this kind of therapy may be further enhanced by noninvasive brain stimulation as shown by a recent study using anodal tDCS.

A 2014 Cochrane review sought to determine the effectiveness of occlusion treatment on patients with sensory deprivation amblyopia, but no trials were found eligible to be included in the review. However, good outcomes from occlusion treatment for sensory deprivation amblyopia likely rely on compliance with the treatment.

Suppression may treated with vision therapy, though there is a wide range of opinions on long-term effectiveness between eye care professionals, with little scientific evidence of long-term improvement of suppression, if the underlying cause is not addressed (strabismus, amblyopia, etc.).

Treatment of strabismic or anisometropic amblyopia consists of correcting the optical deficit (wearing the necessary spectacle prescription) and often forcing use of the amblyopic eye, by patching the good eye, or instilling topical atropine in the good eye, or both.

Concerning patching versus atropine, a drawback is seen in using atropine; the drops can have a side effect of creating nodules in the eye which a correctional ointment can counteract. One should also be wary of overpatching or overpenalizing the good eye when treating amblyopia, as this can create so-called "reverse amblyopia". Eye patching is usually done on a part-time schedule of about 4–6 hours a day. Treatment is continued as long as vision improves. It is not worthwhile continuing to patch for more than 6 months if no improvement continues. Treatment of individuals age 9 through to adulthood is possible through applied perceptual learning.

Deprivation amblyopia is treated by removing the opacity as soon as possible followed by patching or penalizing the good eye to encourage the use of the amblyopic eye. The earlier the treatment is initiated, the easier and faster the treatment is and the less psychologically damaging. Also, the chance of achieving 20/20 vision is greater if treatment is initiated early.

One of the German public health insurance providers, Barmer, has changed its policy to cover, as of 1 April 2014, the costs for an app for amblyopic children whose condition has so far not improved through patching. The app offers dedicated eye exercises which the patient performs while wearing an eyepatch.

There is no known cure for this syndrome. Patients usually need ophthalmic surgery and may also need dental surgery

Genetic counseling and screening of the mother's relatives is recommended.

Young children with strabismus normally suppress the visual field of one eye (or part of it), whereas adults who develop strabismus normally do not suppress and therefore suffer from double vision (diplopia). This also means that adults (and older children) have a higher risk of post-operative diplopia after undergoing strabismus surgery than young children. Patients who have undergone strabismus surgery at a young age often have monofixation syndrome (with peripheral binocular fusion and a central suppression scotoma).

The prognosis for each patient with esotropia will depend upon the origin and classification of their condition. However, in general, management will take the following course:

1. Identify and treat any underlying systemic condition.

2. Prescribe any glasses required and allow the patient time to 'settle into' them.

3. Use occlusion to treat any amblyopia present and encourage alternation.

4. Where appropriate, orthoptic exercises can be used to attempt to restore binocularity.

5. Where appropriate, prismatic correction can be used, either temporarily or permanently, to relieve symptoms of double vision.

6. In specific cases, and primarily in adult patients, botulinum toxin can be used either as a permanent therapeutic approach, or as a temporary measure to prevent contracture of muscles prior to surgery

7. Where necessary, extra-ocular muscle surgery can be undertaken to improve cosmesis and, on occasion, restore binocularity.

The number of cases is around 0.5 to 0.7 per 10,000 births, making it a relatively rare condition.

When strabismus is congenital or develops in infancy, it can cause amblyopia, in which the brain ignores input from the deviated eye. Even with therapy for amblyopia, stereoblindness may occur. The appearance of strabismus may also be a cosmetic problem. One study reported 85% of adult strabismus patients "reported that they had problems with work, school, and sports because of their strabismus." The same study also reported 70% said strabismus "had a negative effect on their self-image." A second operation is sometimes required to straighten the eyes.

Medication is used for strabismus in certain circumstances. In 1989, the US FDA approved Botulinum toxin therapy for strabismus in patients over 12 years old. Most commonly used in adults, the technique is also used for treating children, in particular children affected by infantile esotropia. The toxin is injected in the stronger muscle, causing temporary and partial paralysis. The treatment may need to be repeated three to four months later once the paralysis wears off. Common side effects are double vision, droopy eyelid, overcorrection, and no effect. The side effects typically resolve also within three to four months. Botulinum toxin therapy has been reported to be similarly successful as strabismus surgery for people with binocular vision and less successful than surgery for those who have no binocular vision.

Ametropic amblyopia, is a medical condition in which the retina cannot focus on the image of a distant object, a condition often described as reduced visual acuity. This is due to large uncorrected refractive errors in the patient's optic system of the eyes. Astigmatism is one of the most frequent causes of ametropic amblyopia.

Treatment for this condition entails surveillance of growth and contractures. Furthermore the following are treatment options:

- Thyroid hormone replacement

- Speech therapy

- Hearing aids

"Congenital esotropia," or "infantile esotropia," is a specific sub-type of primary concomitant esotropia. It is a constant esotropia of large and consistent size with onset between birth and six months of age. It is not associated with hyperopia, so the exertion of accommodative effort will not significantly affect the angle of deviation. It is, however, associated with other ocular dysfunctions including oblique muscle over-actions, Dissociated Vertical Deviation (DVD,) Manifest Latent Nystagmus, and defective abduction, which develops as a consequence of the tendency of those with infantile esotropia to 'cross fixate.' Cross fixation involves the use of the right eye to look to the left and the left eye to look to the right; a visual pattern that will be 'natural' for the person with the large angle esotropia whose eye is already deviated towards the opposing side.

The origin of the condition is unknown, and its early onset means that the affected individual's potential for developing binocular vision is limited. The appropriate treatment approach remains a matter of some debate. Some ophthalmologists favour an early surgical approach as offering the best prospect of binocularity whilst others remain unconvinced that the prospects of achieving this result are good enough to justify the increased complexity and risk associated with operating on those under the age of one year.

Nance–Horan syndrome is a rare X linked syndrome characterized by congenital cataract leading to profound vision loss, characteristic dysmorphic features and dental anomalies. Microcornea, microphthalmia and mild or moderate mental retardation may accompany these features. Heterozygous females often manifest similarly but with less severe features than affected males.

Kaufman oculocerebrofacial syndrome is an autosomal recessive congenital disorder characterized by mental retardation, brachycephaly, upslanting palpebral fissures, eye abnormalities, and highly arched palate. It was characterized in 1971; eight cases had been identified as of 1995.

There is currently no cure for GAPO syndrome, but some options are available to reduce the symptoms. Nearsightedness, which affects some sufferers of the disease, can be treated by corrective lenses. Unfortunately, optic atrophy as a result of degradation of the optic nerve (common with GAPO syndrome) cannot be corrected. Corticosteroids have been proposed as a treatment for optic nerve atrophy, but their effectiveness is disputed, and no steroid based treatments are currently available.

The physical abnormalities resulting from SCS are typically mild and only require a minor surgical procedure or no procedure at all. One of the common symptoms of SCS is the development of short (brachydactyly), webbed fingers and broad toes (syndactyly). These characteristics do not cause any problems to the function of the hands or feet, and thus, no medical procedure is required to fix the abnormalities, unless the patient requests it. Webbing of the fingers may affect the base of the fingers, resulting in delayed hand growth during childhood, but this contributes no functional impairments. Sometimes, individuals with SCS develop broad toes because the bones at the ends of the toes are duplicating themselves. This is especially seen in the big toe, but requires no surgical intervention because it doesn't negatively affect the overall function of the foot. Individuals with these toe abnormalities walk normally and can wear normal footwear.

In more severe cases, frequent surgeries and clinical monitoring are required throughout development. A child born with asymmetrical unilateral coronal synostosis should undergo cranioplasty within its first year of life in order to prevent increased intracranial pressure and to prevent progressive facial asymmetry. Cranioplasty is a surgical procedure to correct prematurely fused cranial bones. The surgery acts to reconstruct and reposition the bones and sutures in order to promote the most normal growth. Cranioplasty is necessary in order to continue to grow and is important for two main reasons. First of all, the skull needs to be able to accommodate the growing brain following childbirth, which it can't because the skull doesn't grow as fast as the brain as long as the sutures remain fused. This results in an increase in pressure surrounding the brain and inhibits the brain from growing, causing the individual to experience significant problems, and if left untreated can eventually lead to death. Secondly, cranioplasty may be required for appearance purposes. This is especially the case in individuals with asymmetrical unilateral coronal synostosis, which requires reconstructive surgery of the face and skull. If cranioplasty is not performed, especially in individuals with unilateral coronal synostosis, then facial asymmetry will get worse and worse over time, which is why cranioplasty should be performed as soon as possible.

Surgery may also be required in individuals with vision problems. Vision problems usually arise due to a lack of space in the eye orbit and skull because of the abnormal bone structure of the face. Decreased space may also lead to abnormal or missing tear ducts and nerve damage. Reconstructive surgery is usually required in order to increase cranial space, correct tear duct stenosis, and/or correct ptosis of the eyelids in order to prevent amblyopia (lazy eye).

Midfacial surgery may also be required during early childhood to correct respiratory problems, dental malocclusion, and swallowing difficulties. A cleft palate is also corrected with surgery, and may involve the use of tympanostomy tubes. If needed, an individual will undergo orthognathic treatment and/or orthodontic treatment after facial development is complete. Since hearing loss is frequently associated with SCS, it is recommended that audiology screening persist throughout childhood.

After cranial reconstructive surgery, a child may be required to wear a molding helmet or some other form of head protection until the cranial bones set into place. This typically takes about three months and depends on the child's age and the severity of the condition. Following recovery, individuals with SCS look and act completely normal, so no one would even be able to tell that they have SCS.

Treatment for MSS is symptomatic and supportive including physical and occupational therapy, speech therapy, and special education. Cataracts must be removed when vision is impaired, generally in the first decade of life. Hormone replacement therapy is needed if hypogonadism is present.

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.

DeSanctis–Cacchione syndrome is an extremely rare disorder characterized by the skin and eye symptoms of xeroderma pigmentosum (XP) occurring in association with microcephaly, progressive mental retardation, retarded growth and sexual development, deafness, choreoathetosis, ataxia and quadriparesis.

To treat the trigonocephaly, expanding the distance between orbits using springs seems to work. It allows enough space for the brain to grow and it creates a normal horizontal axis of the orbits and supraorbital bar. The endoscopic surgery started to become popular since the early 90's, but it has some technical limitations (only strip cranictomy is possible). There have been few attempts to go beyond the limits.

Aesthetic outcomes of metopic surgery have been good. Surgery does not have a perfect outcome because there will most likely be minor irregularities. Sometimes reoperations are needed for the severe cases. Trying to hollow out the temporal, and the hypoterlorism are very hard to correct. The hypotelorism usually stays not corrected and in order to correct the temporal hollowing, a second operation is most likely needed.

Treatments are usually based on the individuals symptoms that are displayed. The seizures are controlled with anticonvulsant medication. For the behavior problems, the doctors proscribe to a few medications and behavioral modification routines that involve therapists and other types of therapy. Even if mental retardation is severe, it does not seem to shorten the lifespan of the patient or to get worse with age.

The recurrence of DOOR in siblings and the finding of DOOR syndrome in a few families with consanguinity suggest that the condition is an autosomal recessive genetic condition. Mutations in TBC1D24 have been identified in 9 families.

SCS is the most common craniosynostosis syndrome and affects 1 in every 25,000 to 50,000 individuals. It occurs in all racial and ethnic groups, and affects males and females equally. If a parent carries a copy of the SCS gene mutation, then there is a 50% chance their child will also carry a copy of the gene mutation, in which case, the child may or may not show signs of SCS. There is also a 50% chance their child will have two working copies of the gene, and would therefore, not have SCS. If both parents carry a single copy of the SCS gene mutation, then there is a 25% chance their child will have two gene mutation copies (so child would develop severe SCS), a 25% chance their child would have two normal copies of the gene (so would be completely normal), and a 50% chance their child would carry one gene mutation copy and 1 normal copy (so child may or may not display SCS). In rare situations, two normal parents can have a child with SCS due to a "de novo" mutation. The exact cause of the "de novo" mutation is unknown, but it doesn't seem to be related to anything that the parents did or didn't do during the pregnancy. SCS due to a "de novo" mutation is so rare that the proportion of past cases is unknown.

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.