Currently, the only effective treatment for encephaloceles is reparative surgery, generally performed during infancy. The extent to which it can be corrected depends on the location and size of the encephaloceles; however, large protrusions can be removed without causing major disability. Surgery repositions the bulging area back into the skull, removes the protrusions, and corrects the deformities, typically relieving pressure that can delay normal brain development. Occasionally, shunts are placed to drain excess cerebrospinal fluid from the brain.

The goals of treatment include:

- closure of open skin defects to prevent infection and desiccation of brain tissue

- removal of nonfunctional extracranial cerebral tissue with water-tight closure of the dura

- total craniofacial reconstruction with particular emphasis on avoiding the long-nose deformity (nasal elongation that results from depression of the cribiform plate and nasal placode). Without proper management, the long-nose deformity can be more obvious after repair.

Treatments of NTDs depends on the severity of the complication. No treatment is available for anencephaly and infants usually do not survive more than a few hours. Aggressive surgical management has improved survival and the functions of infants with spina bifida, meningoceles and mild myelomeningoceles. The success of surgery often depends on the amount of brain tissue involved in the encephalocele. The goal of treatment for NTDs is to allow the individual to achieve the highest level of function and independence. Fetal surgery in utero before 26 weeks gestation has been performed with some hope that there is benefit to the final outcome including a reduction in Arnold–Chiari malformation and thereby decreases the need for a ventriculoperitoneal shunt but the procedure is very high risk for both mother and baby and is considered extremely invasive with questions that the positive outcomes may be due to ascertainment bias and not true benefit. Further, this surgery is not a cure for all problems associated with a neural tube defect. Other areas of research include tissue engineering and stem cell therapy but this research has not been used in humans.

Pregnant mothers are advised to take folic acid supplements to reduce risk of iniencephaly by up to 70%. Pregnant mothers are also advised not to take antiepileptic drugs, diuretics, antihistamines, and sulfa drugs, all of which have been associated with increased risk for neural tube defects.

It is recommended that women who may become pregnant take 400 micrograms of folic acid daily.

Standard treatment is after delivery. There is tentative evidence about treatment for severe disease before delivery while the baby is inside the womb. As of 2014 the evidence; however, remains insufficient to determine benefits and harms.

Treatment of spina bifida during pregnancy is not without risk. To the mother, this includes scarring of the uterus. To the baby, there is the risk of preterm birth.

Broadly, there are two forms of prenatal treatment. The first is open fetal surgery, where the uterus is opened and the spina bifida repair performed. The second is via fetoscopy. These techniques may be an option to standard therapy.

Most individuals with myelomeningocele will need periodic evaluations by a variety of specialists:

- Physiatrists coordinate the rehabilitation efforts of different therapists and prescribe specific therapies, adaptive equipment, or medications to encourage as high of a functional performance within the community as possible.

- Orthopedists monitor growth and development of bones, muscles, and joints.

- Neurosurgeons perform surgeries at birth and manage complications associated with tethered cord and hydrocephalus.

- Neurologists treat and evaluate nervous system issues, such as seizure disorders.

- Urologists to address kidney, bladder, and bowel dysfunction – many will need to manage their urinary systems with a program of catheterization. Bowel management programs aimed at improving elimination are also designed.

- Ophthalmologists evaluate and treat complications of the eyes.

- Orthotists design and customize various types of assistive technology, including braces, crutches, walkers, and wheelchairs to aid in mobility. As a general rule, the higher the level of the spina bifida defect, the more severe the paralysis, but paralysis does not always occur. Thus, those with low levels may need only short leg braces, whereas those with higher levels do best with a wheelchair, and some may be able to walk unaided.

- Physical therapists, occupational therapists, psychologists, and speech/language pathologists aid in rehabilitative therapies and increase independent living skills.

In 1996, the United States Food and Drug Administration published regulations requiring the addition of folic acid to enriched breads, cereals, flour and other grain products. It is important to note that during the first four weeks of pregnancy (when most women do not even realize that they are pregnant), adequate folate intake is essential for proper operation of the neurulation process. Therefore, women who could become pregnant are advised to eat foods fortified with folic acid or take supplements in addition to eating folate-rich foods to reduce the risks of serious birth defects.

In Canada, mandatory fortification of selected foods with folic acid has been shown to reduce the incidence of neural tube defects by 46%.

Women who may become pregnant are advised to get 400 micrograms of folic acid daily. Women who have previously given birth to a child with a neural tube defect may benefit from a supplement containing 4.0 mg/5.0 mg in the UK mg daily, following advice provided by their doctor.

Since newborns with iniencephaly so rarely survive past childbirth, a standard treatment does not exist.

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.

To correct the rather prominent hypertelorism, wide nasal root and midline cleft in FND, a facial bipartition can be performed. This surgery is preferred to periorbital box-osteotomy because deformities are corrected with a better aesthetic result.

During the operation, the orbits are disconnected from the skull and the base of the skull. However, they remain attached to the upper jaw. Part of the forehead in the centre of the face is removed (median faciotomy) in the process. Then, the orbits are rotated internally, to correct the hypertelorism. Often, a new nasal bone will have to be interpositioned, using a bone transplant.

Complications of this procedure are: bleeding, meningitis, cerebrospinal fluid leakage and blindness.

Because this malformation is rare and there are extremely few individuals living with this condition, treatment is limited. Treatment consists of carefully managing the condition in a controlled manner. Proceeding with a bone graft when the child reaches school age is also recommended.

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.

Although surgery is the treatment of choice, it must be preceded by imaging studies to exclude an intracranial connection. Potential complications include meningitis and a cerebrospinal fluid leak. Recurrences or more correctly persistence may be seen in up to 30% of patients if not completely excised.

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.

The surgery takes place under general anaesthesia and lasts less than 1 hour. The surgeon prepares the locus to the size of the implant after performing a 8-cm axillary incision and inserts the implant beneath the skin. The closure is made in 2 planes.

The implant will replace the pectoralis major muscle, thus enabling the thorax to be symmetrical and, in women, the breast as well. If necessary, especially in the case of women, a second operation will complement the result by the implantation of a breast implant and / or lipofilling.

Lipomodelling is progressively used in the correction of breast and chest wall deformities. In Poland syndrome, this technique appears to be a major advance that will probably revolutionize the treatment of severe cases. This is mainly due to its ability to achieve previously unachievable quality of reconstruction with minimal scaring.

The complete or partial absence of the pectoralis muscle is the malformation that defines Poland Syndrome. It can be treated by inserting a custom implant designed by CAD (computer aided design). A 3D reconstruction of the patient's chest is performed from a medical scanner to design a virtual implant perfectly adapted to the anatomy of each one. The implant is made of medical silicone unbreakable rubber. This treatment is purely cosmetic and does not make up for the patient's imbalanced upper body strength.

The Poland syndrome malformations being morphological, correction by custom implant is a first-line treatment. This technique allows a wide variety of patients to be treated with good outcomes. Poland Syndrome can be associated with bones, subcutaneous and mammary atrophy: if the first, as for pectus excavatum, is successfully corrected by a custom implant, the others can require surgical intervention such as lipofilling or silicone breast implant, in a second operation.

Probably, the most well-known teratogenic drug is thalidomide. It was developed near the end of the 1950s by Chemie Grűnenthal as a sleep inducing aid and antiemetic. Because of its ability to prevent nausea it was prescribed for pregnant women in almost 50 countries worldwide between 1956–1962. Until William McBride published the study leading to its withdrawal from the market at 1961, about 8- 10 000 severely malformed children were born. The most typical disorder induced by thalidomide were reductional deformities of the long bones of the extremities. Phocomelia otherwise a rare deformity, which therefore helped to recognise the teratogenic effect of the new drug. Among other malformations caused by thalidomide were those of ears, eyes, brain, kidney, heart, digestive and respiratory tract. 40% of the prenatally affected children died soon after birth. As thalidomide is used today as a treatment for multiple myeloma and leprosy, several births of affected children were described in spite of the strictly required use of contraception among female patients treated by it.

Vitamin A, or retinol, is the sole vitamin which is embryotoxic even in a therapeutic dose, for example in multivitamins, because its metabolite, the retinoic acid, plays an important role as a signal molecule in the development of several tisues and organs. Its natural precursor, the β-carotene, is considered safe, whereas the consumption of animal liver can lead to malformation, as the liver stores lipophile vitamins, including retinol. Isotretinoin (13-cis-retinoic-acid; brand name Roaccutane), vitamine A analog, which is often used to treat severe acne, is such a strong teratogen that just a single dose taken by a pregnant woman (even transdermally) may result in serious birth defects. Because of this effect, most countries have systems in place to ensure that it is not given to pregnant women, and that the patient is aware of how important it is to prevent pregnancy during and at least one month after treatment. Medical guidelines also suggest that pregnant women should limit vitamin A intake to about 700 μg/day, as it has teratogenic potential when consumed in excess. Vitamine A and similar substances can induce spontaneous abortions, premature births, defects of eyes (microphthalmia), ears, thymus, face deformities, neurological (hydrocephalus, microcephalia) and cardiovascular defects, as well as mental retardation.

Tetracycline, an antibiotic, should never be prescribed to women in the reproductive age or children, because of its negative impact on bone mineralization and teeth mineralization. The "tetracycline teeth" have brown or grey colour as a result of a defective development of both the dentine and the enamel of teeth.

Several anticonvulsants are known to be highly teratogenic. Phenytoin, also known as diphenylhydantoin, along with carbamazepine is responsible for the fetal hydantoin syndrome, which may typically include broad nose base, cleft lip and/or palate, microcephalia, nails and fingers hypoplasia, intrauterine growth restriction and mental retardation. Trimethadione taken during pregnancy is responsible for the fetal trimethadione syndrome, characterized by craniofacial, cardiovascular, renal and spine malformations, along with a delay in mental and physical development. Valproate has anti-folate effects, leading to neural tube closure-related defects such as spina bifida. Lower IQ and autism have recently also been reported as a result of intrauterine valproate exposure.

Hormonal contraception is considered as harmless for the embryo. Peterka and Novotná do however state that syntethic progestines used to prevent miscarriage in the past frequently caused masculinization of the outer reproductive organs of female newborns due to their androgenic activity. Diethylstilbestrol is a synthetic estrogen used from the 1940s to 1971 when the prenatal exposition has been linked to the clear-cell adenocarcinoma of the vagina. Following studies showed elevated risks for other tumors and congenital malformations of the sex organs for both sexes.

All cytostatics are strong teratogens, abortion is usually recommended when pregnancy is found during or before chemotherapy. Aminopterin, a cytostatic drug with anti-folate effect, was used during the 1950s and 1960s to induce therapeutic abortions. In some cases the abortion didn´t happen, but the newborns suffered a fetal aminopterin syndrome consisting of growth retardation, craniosynostosis, hydrocephalus, facial dismorphities, mental retardation and/or leg defomities

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.

Usually babies with this malformation do not survive past birth. However, there have been cases of survival. As of 2004, there were only two reported living cases. Of these two, one was severely cognitively impaired and physically disabled. The status of the other was unreported. If the fetus progresses to full term, there is the risk that it will have head trauma from the pressure applied to the head while being delivered. A few other cases of acalvaria have been reported, which did not progress to birth. In addition to the lack skull cap, there were brain malformations present in each case, and all of the pregnancies were terminated either electively or the fetuses were spontaneously aborted.

No specific treatment is available. Management is only supportive and preventive.

Those who are diagnosed with the disease often die within the first few months of life. Almost all children with the disease die by the age of three.

A birth defect, also known as congenital disorder, is a condition present at birth regardless of cause. They may result in health problems such as physical disability, intellectual disability, or developmental disability. Severity may vary from mild to severe. They are divided into two main types: structural birth defects in which there is problems with the shape of a body part and functional birth defects in which there is problems with how a body part works. Some birth defects include problems of both types.

Birth defects may result from genetic or chromosomal problems, exposure to certain medications or chemicals, or certain infections during pregnancy. Risk factors include not enough folic acid, drinking alcohol or smoking during pregnancy, poorly controlled diabetes, and a mother over the age of 35 years old. Many are believed to involve a number of factors. Birth defects may be visible at birth or diagnosed by screening tests.

Treatment varies depending on the defect in question. This may include therapy, medication, surgery, or assistive technology. Birth defects affected about 96 million people as of 2015. In the United States they occur in about 3% of newborns. They resulted in about 628,000 deaths in 2015 down from 751,000 in 1990. The types with the greatest numbers of deaths are congenital heart disease (303,000), followed by neural tube defects (65,000).

Prosthesis is a synthetic alternative for missing limbs, teeth, and various other body parts. Advances in prosthetic limbs have increased greatly during the twentieth century. The use of new materials such as modern plastics, complex procedures and better pigments have created lighter in weight and more realistic looking artificial limbs. With the advancement of myoelectric prosthetic limbs, patients are able to move their limbs without the use of cords or other devices. The myoelectric limbs can detect electric signals from the nervous system and muscles. They were first used on adults, but now they are being fitted to children.

Patients that receive a loss of limbs due to phocomelia are typically treated with prosthetics. Infants at the age of 6 months are recommended to have a prosthetic mitten fitted; enabling them to get used to the prosthesis. A hook will be added when the child reaches the age of 2 years. Eventually the patient may receive a myoelectric prosthetic limb. Patients are treated in this way due to the lack of understanding at a young age and the absence of necessary tissues and bones to hold the prosthetic limb.

Limb body wall complex (LBWC) is a rare fetal malformation of unknown origins.

Traditionally diagnosis has been based on the Van Allen et al., criteria, i.e. the presence of two out of three of the following anomalies:

1. Exencephaly or encephalocele with facial clefts

2. Thoraco and or abdominoschisis and

3. Limb defects.

LBWC occurs in approximately 0.32 in 100,000 births.

At this time, there is no known cause of Limb Body Wall Complex. However, there have been tentative links made between a diagnosis of LBWC and cocaine use. In addition, current research has shown that there may be a genetic cause for a small limited number of LBWC cases.

Limb Body Wall Complex is a lethal birth defect. There are only anecdotal stories of survivors.

While nasal glial heterotopia (NGH) is the preferred term, synonyms have included nasal glioma. However, this term is to be discouraged, as it implies a neoplasm or tumor, which it is not. By definition, nasal glial heterotopia is a specific type of choristoma. It is not a teratoma, however, which is a neoplasm comprising all three germ cell layers (ectoderm, endoderm, mesoderm). As a congenital malformation or ectopia, it is distinctly different from the trauma or iatrogenic development of an encephalocele.

Timo cysts may spontaneously resolve or with pressure directed toward the nose; however, nasolacrimal duct probing may be required to open the obstruction.