Temporary alleviation can be achieved by inserting an oral airway into the mouth. However, the only definitive treatment is surgery to correct the defect by perforating the atresia to create a nasopharyngeal airway. If the blockage is caused by bone, this is drilled through and stent inserted. The patient has to have this sucked out by an air vacuum machine . And in later life as a teenager or in early twenties the hole will have to be re-drilled larger.

A stent may be inserted to keep the newly formed airway patent or repeated dilatation may be performed.

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.

Although rare, this condition is often treatable with surgery. In most cases, the blind hemivagina is opened, and the fluid drained.

The objective of irradiation is to halt the growth of the acoustic neuroma tumour, it does not excise it from the body, as the term 'radiosurgery' or 'gammaknife' implies. Radiosurgery is only suitable for small to medum size tumors.

There are three modalities of surgical treatment (excision) depending on where the anatomical location of the incision to access the tumor is made: retrosigmoid (a variant of what was formerly called suboccipital), translabyrinthine, and middle fossa.

The goals of surgery are to control the tumor, and preserve hearing as well as facial nerves. Especially in the case of larger tumors, there may be a tradeoff between tumor removal and preservation of nerve functionality.

There are different defined degrees of surgical excision, termed 'subtotal resection', 'radical subtotal resection', 'near-total resection', and 'total resection' in order or increasing proportion of tumor removed. Lesser amount of tumor removal may increase likelihood of preservation of nerve function (hence better post-operative hearing), but also likelihood of tumor regrowth, necessitating additional treatment.

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.

There is no treatment to correct an enlarged vestibular aqueduct. Any hearing loss will need management with amplification and support in education and at work. If the hearing loss becomes severe to profound cochlear implants can be of significant value. Vestibular disturbance is usually short-lived and associated with head trauma but significant vestibular hypofunction may require rehabilitation.

People with enlarged vestibular aqueducts are advised to avoid head trauma where possible. This usually means avoiding contact sports such as boxing and rugby, but also horse riding, trampolining and other sports where head injury may occur. Some have symptoms when flying and should limit these activities if affected.

MCDK is not treatable. However, the patient is observed periodically for the first few years during which ultrasounds are generally taken to ensure the healthy kidney is functioning properly and that the unhealthy kidney is not causing adverse effects. In severe cases MCDK can lead to neonatal fatality (in bilateral cases), however in unilateral cases the prognosis might be better (it would be dependent on associated anomalies).

Treatment for cystic hygroma involves the removal of the abnormal tissue; however complete removal may be impossible without removing other normal areas. Surgical removal of the tumor is the typical treatment provided, with the understanding that additional removal procedures will most likely be required as the lymphangioma grows. Most patients need at least two procedures done for the removal process to be achieved. Recurrence is possible but unlikely for those lesions able to be removed completely via excisional surgery. Radiotherapy and chemical cauteries are not as effective with the lymphangioma than they are with the hemangioma. Draining lymphangiomas of fluid provides only temporary relief, so they are removed surgically. Cystic Hygroma can be treated with OK432 (Picibanil).

The least invasive and most effective form of treatment is now performed by interventional radiologists. A sclerosing agent, such as 1% or 3% sodium tetradecyl sulfate, doxycycline, or ethanol, may be directly injected into a lymphocele. "All sclerosing agents are thought to work by ablating the endothelial cells of the disrupted lymphatics feeding into the lymphocele."

Lymphangioma circumscription can be healed when treated with a flashlamp pulsed dye laser, although this can cause port-wine stains and other vascular lesions.

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.

Very few risk factors for choanal atresia have been identified. While causes are unknown, both genetic and environmental triggers are suspected. One study suggests that chemicals that act as endocrine disrupters may put an unborn infant at risk. A 2012 epidemiological study looked at atrazine, a commonly used herbicide in the U.S., and found that women who lived in counties in Texas with the highest levels of this chemical being used to treat agricultural crops were 80 times more likely to give birth to infants with choanal atresia or stenosis compared to women who lived in the counties with the lowest levels. Another epidemiological report in 2010 found even higher associations between increased incidents of choanal atresia and exposure to second-hand-smoke, coffee consumption, high maternal zinc and B-12 intake and exposure to anti-infective urinary tract medications.

In general, the younger the child, the greater the urgency in removing the cataract, because of the risk of amblyopia. For optimal visual development in newborns and young infants, a visually significant unilateral congenital cataract should be detected and removed before age 6 weeks, and visually significant bilateral congenital cataracts should be removed before age 10 weeks.

Some congenital cataracts are too small to affect vision, therefore no surgery or treatment will be done. If they are superficial and small, an ophthalmologist will continue to monitor them throughout a patient's life. Commonly, a patient with small congenital cataracts that do not affect vision will eventually be affected later in life; generally this will take decades to occur.

A child with posterior crossbite should be treated immediately if the child shifts his mandible on closing which is often seen in a unilateral crossbite as mentioned above. The best age to treat a child with crossbite is in their mixed dentition when their palatal sutures have not fused to each other. Palatal expansion allows more space in an arch to relieve crowding and correct posterior crossbite. The correction can include any type of palatal expanders that will expand the palate which resolves the narrow constriction of the maxilla. There are several therapies that can be used to correct a posterior crossbite: braces, 'Z' spring or cantilever spring, quad helix, removable plates, clear aligner therapy, or a Delaire mask. The correct therapy should be decided by the orthodontist depending on the type and severity of the crossbite.

One of the keys in diagnosing the anterior crossbite due to skeletal vs dental causes is diagnosing a CR-CO shift in a patient. An adolescent presenting with anterior crossbite may be positioning their mandible forward into centric occlusion (CO) due to the dental interferences. Thus finding their occlusion in centric relation (CR) is key in diagnosis. For anterior crossbite, if their CO matches their CR then the patient truly has a skeletal component to their crossbite. If the CR shows a less severe class 3 malocclusion or teeth not in anterior crossbite, this may mean that their anterior crossbite results due to dental interferences.

Goal to treat unilateral crossbites should definitely include removal of occlusal interferences and elimination of the functional shift. Treating posterior crossbites early may help prevent the occurrence of Temporomandibular joint pathology.

Unilateral crossbites can also be diagnosed and treated properly by using a Deprogramming splint. This splint has flat occlusal surface which causes the muscles to deprogram themselves and establish new sensory engrams. When the splint is removed, a proper centric relation bite can be diagnosed from the bite.

Hemifacial hypertrophy (also termed facial hemihypertrophy, facial hemihyperplasia, or Friedreich's disease) abbreviated as (HFH) is rare congenital disease characterized by unilateral enlargement of the head and teeth. It is classified as true HFH (THFH) with unilateral enlargement of the viscerocranium, and partial HFH (PHFH) in which not all structures are enlarged. Hemifacial hypertrophy can cause a wide spectrum of defects or may involve only muscle or bone. it is usually treated surgically. It is believed to be a minor form of hemihypertrophy.

Treatment of Foix–Chavany–Marie syndrome depends on the onset of symptoms and involves a multidisciplinary approach. Drugs are used in neurological recovery depending on the etiological classification of FCMS. FCMS caused by epilepsy, specifically resulting in the development of lesions in the bilateral and subcortical regions of the brain can be treated using antiepileptic drugs to reverse abnormal EEG changes and induce complete neurological recovery. In addition, a hemispherectomy can be performed to reverse neurological deficits and control the seizures. This procedure can result in a complete recovery from epileptic seizures. Physical therapy is also used to manage symptoms and improve quality of life. Classical FCMS resulting in the decline of ones ability to speak and swallow can be treated using neuromuscular electrical stimulation and traditional dysphagia therapy. Speech therapy further targeting dysphagia can strengthen oral musculature using modified feeding techniques and postures. Therapeutic feedings include practicing oral and lingual movements using ice chips. In addition, different procedures can be performed by a neurosurgeon to alleviate some symptoms.

The condition is often diagnosed through an MRI or ultrasound. Consulting a specialist (in this case a gynecologist) is recommended.

Spectacles or RGP contact lenses can be used to manage the astigmatism. when the condition worsens, surgical correction may be required.

Congenital cystic eye (also known as "CCE" or "cystic eyeball") is an extremely rare ocular malformation where the eye fails to develop correctly "in utero" and is replaced by benign, fluid-filled tissue. Its incidence is unknown, due to the very small number of cases reported. An audit by Duke-Elder of the medical literature from 1880 to 1963 discovered only 28 cases. The term was coined in 1937 by the renowned ophthalmologist Ida Mann.

Embryologically, the defect is thought to occur around day 35 of gestation, when the vesicle fails to invaginate. Dysgenesis of the vesicle later in development may result in coloboma, a separate and less severe malformation of the ocular structures.

CCE is almost always unilateral, but at least 2 cases of bilateral involvement have been described. Patients may also present with skin appendages attached to the skin surrounding the eyes. Association with intracranial anomalies has been reported.

Treatment of CCE is usually by enucleation, followed by insertion of an ocular implant and prosthesis.

The prognosis for lymphangioma circumscriptum and cavernous lymphangioma is generally excellent. This condition is associated with minor bleeding, recurrent cellulitis, and lymph fluid leakage. Two cases of lymphangiosarcoma arising from lymphangioma circumscriptum have been reported; however, in both of the patients, the preexisting lesion was exposed to extensive radiation therapy.

In cystic hygroma, large cysts can cause dysphagia, respiratory problems, and serious infection if they involve the neck. Patients with cystic hygroma should receive cytogenetic analysis to determine if they have chromosomal abnormalities, and parents should receive genetic counseling because this condition can recur in subsequent pregnancies.

Complications after surgical removal of cystic hygroma include damage to the structures in the neck, infection, and return of the cystic hygroma.

Literature states that very few crossbites tend to self-correct which often justify the treatment approach of correcting these bites as early as possible. Only 0–9% of crossbites self-correct. Lindner et al. reported that in a 50% of crossbites were corrected in 76 four year old children.

Maxillary lateral incisor agenesis (MLIA) is lack of development (agenesis) of one or both of the maxillary lateral incisor teeth. In normal human dentition, this would be the second tooth on either side from the center of the top row of teeth. The condition is bilateral if the incisor is absent on both sides or unilateral if only one is smissing. It appears to have a genetic component.

If the nematode can be seen by an ophthalmologist, which occurs in less than half of cases, it should be treated with photocoagulation for extramacular location and surgical removal in case the larva is lying in the macula. After the worm is killed, visual acuity loss usually does not progress. Alternatively, Antihelminthic treatment such as high dose oral Albendazole and prednisolone may be used.

Incontinentia pigmenti achromians (also known as "hypomelanosis of Ito") is a cutaneous condition characterized by various patterns of bilateral or unilateral hypopigmentation following the lines of Blaschko. Though the consistency of the skin findings have led to the term "hypomelanosis of Ito", it actually refers to a group of disorders with various genetic causes including polyploidies and aneuploidies. Based upon the specifics of the genetic defect, the skin findings can be accompanied by a great range of systemic findings. These include central nervous system, ocular, and musculoskeletal defects. Nonetheless, the vast majority of cases are limited to the skin. As opposed to incontinentia pigmenti, hypomelanosis of Ito affects both genders equally.

Segmental odontomaxillary dysplasia is a painless, unilateral enlargement of the upper jaw. The cause is unknown, and the disease affects the jaws, teeth, and adjacent soft tissue. The premolars may be congenitally missing, and the primary teeth (baby teeth) may be smaller than usual. It is a relatively recent discovery.

Because MLIA can be detected from partial skeletal remains, it is useful in the field of anthropology. Anthropologically-interesting human remains often have relatively well preserved skeletons, but no soft tissues or intact DNA. This makes it hard to determine relationships between the deceased individuals. MLIA is sometimes related to inbreeding, so the presence of MLIA in many members of a large collection of remains can indicate that the population that lived there was relatively inbred. This technique has been used to study a group of Neolithic farmers.