A deficiency of folate itself does not cause neural tube defects. The association seen between reduced neural tube defects and folic acid supplementation is due to a gene-environment interaction such as vulnerability caused by the C677T Methylenetetrahydrofolate reductase (MTHFR) variant. Supplementing folic acid during pregnancy reduces the prevalence of NTDs by not exposing this otherwise sub-clinical mutation to aggravating conditions. Other potential causes can include folate antimetabolites (such as methotrexate), mycotoxins in contaminated corn meal, arsenic, hyperthermia in early development, and radiation. Maternal obesity has also been found to be a risk factor for NTDs. Studies have shown that both maternal cigarette smoking and maternal exposure to secondhand smoke increased the risk for neural tube defects in offspring. A mechanism by which maternal exposure to cigarette smoke could increase NTD risk in offspring is suggested by several studies that show an association between cigarette smoking and elevations of homocysteine levels. Cigarette smoke during pregnancy, including secondhand exposure, can increase the risk of neural tube defects. All of the above may act by interference with some aspect of normal folic acid metabolism and folate linked methylation related cellular processes as there are multiple genes of this type associated with neural tube defects.

A low socioeconomic status in a deprived neighborhood may include exposure to “environmental stressors and risk factors.” Socioeconomic inequalities are commonly measured by the Cartairs-Morris score, Index of Multiple Deprivation, Townsend deprivation index, and the Jarman score. The Jarman score, for example, considers “unemployment, overcrowding, single parents, under-fives, elderly living alone, ethnicity, low social class and residential mobility.” In Vos’ meta-analysis these indices are used to view the effect of low SES neighborhoods on maternal health. In the meta-analysis, data from individual studies were collected from 1985 up until 2008. Vos concludes that a correlation exists between prenatal adversities and deprived neighborhoods. Other studies have shown that low SES is closely associated with the development of the fetus in utero and growth retardation. Studies also suggest that children born in low SES families are “likely to be born prematurely, at low birth weight, or with asphyxia, a birth defect, a disability, fetal alcohol syndrome, or AIDS.” Bradley and Corwyn also suggest that congenital disorders arise from the mother’s lack of nutrition, a poor lifestyle, maternal substance abuse and “living in a neighborhood that contains hazards affecting fetal development (toxic waste dumps).” In a meta-analysis that viewed how inequalities influenced maternal health, it was suggested that deprived neighborhoods often promoted behaviors such as smoking, drug and alcohol use. After controlling for socioeconomic factors and ethnicity, several individual studies demonstrated an association with outcomes such as perinatal mortality and preterm birth.

Substances whose toxicity can cause congenital disorders are called "teratogens", and include certain pharmaceutical and recreational drugs in pregnancy as well as many environmental toxins in pregnancy.

A review published in 2010 identified 6 main teratogenic mechanisms associated with medication use: folate antagonism, neural crest cell disruption, endocrine disruption, oxidative stress, vascular disruption and specific receptor- or enzyme-mediated teratogenesis.

It is estimated that 10% of all birth defects are caused by prenatal exposure to a teratogenic agent. These exposures include, but are not limited to, medication or drug exposures, maternal infections and diseases, and environmental and occupational exposures. Paternal smoking use has also been linked to an increased risk of birth defects and childhood cancer for the offspring, where the paternal germline undergoes oxidative damage due to cigarette use. Teratogen-caused birth defects are potentially preventable. Studies have shown that nearly 50% of pregnant women have been exposed to at least one medication during gestation. During pregnancy, a female can also be exposed to teratogens from the contaminated clothing or toxins within the seminal fluid of a partner. An additional study found that of 200 individuals referred for genetic counseling for a teratogenic exposure, 52% were exposed to more than one potential teratogen.

Folic acid supplementation reduces the prevalence of neural tube defects by approximately 70% of neural tube defects indicating that 30% are not folate-dependent and are due to some cause other than alterations of methylation patterns. Multiple other genes related to neural tube defects exist which are candidates for folate insensitive neural tube defects. There are also several syndromes such as Meckel syndrome, and Triploid Syndrome which are frequently accompanied by neural tube defects that are assumed to be unrelated to folate metabolism

Studies have shown that obesity of the mother increases the risk of neural tube disorders such as iniencephaly by 1.7 fold while severe obesity increases the risk by over 3 fold.

Once a mother has given birth to a child with iniencephaly, risk of reoccurrence increases to 1-5%.

There is neither a single cause of spina bifida nor any known way to prevent it entirely. However, dietary supplementation with folic acid has been shown to be helpful in reducing the incidence of spina bifida. Sources of folic acid include whole grains, fortified breakfast cereals, dried beans, leaf vegetables and fruits.

Folate fortification of enriched grain products has been mandatory in the United States since 1998. The U.S. Food and Drug Administration, Public Health Agency of Canada and UK recommended amount of folic acid for women of childbearing age and women planning to become pregnant is at least 0.4 mg/day of folic acid from at least three months before conception, and continued for the first 12 weeks of pregnancy.

Women who have already had a baby with spina bifida or other type of neural tube defect, or are taking anticonvulsant medication, should take a higher dose of 4–5 mg/day.

Certain mutations in the gene "VANGL1" have been linked with spina bifida in some families with a history of the condition.

Spina bifida is sometimes caused by the failure of the neural tube to close during the first month of embryonic development (often before the mother knows she is pregnant). Some forms are known to occur with primary conditions that cause raised central nervous system pressure, raising the possibility of a dual pathogenesis.

In normal circumstances, the closure of the neural tube occurs around the 23rd (rostral closure) and 27th (caudal closure) day after fertilization. However, if something interferes and the tube fails to close properly, a neural tube defect will occur. Medications such as some anticonvulsants, diabetes, obesity, and having a relative with spina bifida can all affect the probability of neural tube malformation.

Extensive evidence from mouse strains with spina bifida indicates that there is sometimes a genetic basis for the condition. Human spina bifida, like other human diseases, such as cancer, hypertension and atherosclerosis (coronary artery disease), likely results from the interaction of multiple genes and environmental factors.

Research has shown the lack of folic acid (folate) is a contributing factor in the pathogenesis of neural tube defects, including spina bifida. Supplementation of the mother's diet with folate can reduce the incidence of neural tube defects by about 70%, and can also decrease the severity of these defects when they occur. It is unknown how or why folic acid has this effect.

Spina bifida does not follow direct patterns of heredity as do muscular dystrophy or haemophilia. Studies show a woman having had one child with a neural tube defect such as spina bifida has about a 3% risk of having another affected child. This risk can be reduced with folic acid supplementation before pregnancy. For the general population, low-dose folic acid supplements are advised (0.4 mg/day).

Until recently, medical literature did not indicate a connection among many genetic disorders, both genetic syndromes and genetic diseases, that are now being found to be related. As a result of new genetic research, some of these are, in fact, highly related in their root cause despite the widely varying set of medical symptoms that are clinically visible in the disorders. Anencephaly is one such disease, part of an emerging class of diseases called ciliopathies. The underlying cause may be a dysfunctional molecular mechanism in the primary cilia structures of the cell, organelles present in many cellular types throughout the human body. The cilia defects adversely affect "numerous critical developmental signaling pathways" essential to cellular development and, thus, offer a plausible hypothesis for the often multi-symptom nature of a large set of syndromes and diseases. Known ciliopathies include primary ciliary dyskinesia, Bardet-Biedl syndrome, polycystic kidney and liver disease, nephronophthisis, Alström syndrome, Meckel-Gruber syndrome, and some forms of retinal degeneration.

Some genetic research has been conducted to determine the causes of anencephaly. It has been found that cartilage homeoprotein (CART1) is selectively expressed in chondrocytes (cartilage cells). The CART1 gene to chromosome 12q21.3–q22 has been mapped. Also, it has been found that mice homozygous for deficiency in the Cart1 gene manifested acrania and meroanencephaly, and prenatal treatment with folic acid will suppress acrania and meroanencephaly in the Cart1-deficient mutants.

Encephaloceles occur rarely, at a rate of one per 5,000 live births worldwide. Encephaloceles of the back of the head are more common in Europe and North America, while encephaloceles on the front of the head more frequently occur in Southeast Asia, Africa, Malaysia, and Russia. Ethnic, genetic, and environmental factors, as well as parental age, can all affect the likelihood of encephaloceles. The condition can occur in families with a family history of spina bifida.

Prognosis is poor. Previous research suggested a 100% mortality rate for those with acrania. This disease is rare, occurring in 1 in 20,000 live births.

In order to better manage an acrania diagnosis, early detection is of extreme importance so that actions may be taken to help the mother and child. Families may choose either to terminate the pregnancy, or to carry the child to term. Acrania may cause a fetus to spontaneously abort before reaching term.

Recent research has found that Dandy–Walker syndrome often occurs in patients with PHACES syndrome.

Little genetic counseling can be offered for acrania because the genetic origins are not fully understood. In order to make genetic counseling for families easier this disease is often differentially diagnosed with other diseases that can occur at the same time such as anencephaly and acalvaria, though these diseases may not always occur simultaneously. While this disease is tragic, reoccurrence rates are extremely low so genetic counseling is not always necessary.

Until recently, the medical literature did not indicate a connection among many genetic disorders, both genetic syndromes and genetic diseases, that are now being found to be related. As a result of new genetic research, some of these are, in fact, highly related in their root cause (genotype) despite the widely varying set of medical characteristics (phenotype) that are clinically visible in the disorders. Dandy–Walker syndrome is one such disease, part of an emerging class of diseases called ciliopathies. The underlying cause may be a dysfunctional molecular mechanism in the primary cilia structures of the cell, organelles which are present in many cellular types throughout the human body. The cilia defects adversely affect "numerous critical developmental signaling pathways" essential to cellular development and thus offer a plausible hypothesis for the often multi-symptom nature of a large set of syndromes and diseases. Known ciliopathies include primary ciliary dyskinesia, Bardet-Biedl syndrome, polycystic kidney and liver disease, nephronophthisis, Alstrom syndrome, Meckel-Gruber syndrome and some forms of retinal degeneration.

Genetic associations of the condition are being investigated.

Although the exact cause is unknown, encephaloceles are caused by failure of the neural tube to close completely during fetal development. Research has indicated that teratogens (substances known to cause birth defects), trypan blue (a stain used to color dead tissues or cells blue), and arsenic may damage the developing fetus and cause encephaloceles.

Proper levels of folic acid have been shown to help prevent such defects when taken before pregnancy, and early in pregnancy.

Acalvaria usually occurs in less than 1 of every 100,000 births. By way of epidemiological data, it is thought that females are more prone to have this defect. Currently, acalvaria is not thought to have much of a risk of recurrence.

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.

The prevalence of Klippel–Feil syndrome is unknown due to the fact that there was no study done to determine the true prevalence.

Although the actual occurrence for the KFS syndrome is unknown, it is estimated to occur 1 in 40,000 to 42,000 newborns worldwide. In addition, females seem to be affected slightly more often than males.

Genetic genealogy has identified a specific location of a gene on a chromosome for Klippel-Feil Syndrome. Mutations in the GDF6 and GDF3 genes have also been identified to cause the disease, although some people with Klippel–Feil syndrome do not have identified mutations in the GDF6 or GDF3 genes. In this case, the cause of the condition in these individuals is unknown. GDF6 and GDF3 genes provide the body with instructions for making proteins involved in regulating the growth and maturation of bone and cartilage. These proteins actively regulate cell growth in embryonic and adult tissue. GDF6 specifically is involved in the formation of vertebral bones, among others, and establishing boundaries between bones in skeletal development while GDF3 is involved with bone and cartilage growth. Mutations cause reductions in these functional proteins but, it is unclear exactly how a shortage in these proteins leads to incomplete separation of the vertebrae in people with Klippel–Feil syndrome. However, when the GDF6 gene was knocked out in mice, the result was the fusion of bones. Only by identifying the link between the genetic cause and the phenotypic pathoanatomy of Klippel–Feil syndrome will we be able to rationalize the heterogeneity of the syndrome.

These mutations can be inherited in two ways:

- Autosomal dominant inheritance, where one copy of the altered gene in each cell is sufficient to cause the disorder, is especially associated with C2-C3 fusion.

- Autosomal recessive inheritance, where both copies of a gene contain mutations, is especially associated with C5-C6 fusion.

- Another autosomal dominant form (mapped on locus 8q22.2) known as Klippel–Feil syndrome with laryngeal malformation has been identified. It is also known as Segmentation syndrome 1.

The most widely accepted pathophysiological mechanism by which Chiari type I malformations occur is by a reduction or lack of development of the posterior fossa as a result of congenital or acquired disorders. Congenital causes include hydrocephalus, craniosynostosis (especially of the lambdoid suture), hyperostosis (such as craniometaphyseal dysplasia, osteopetrosis, erythroid hyperplasia), X-linked vitamin D-resistant rickets, and neurofibromatosis type I. Acquired disorders include space occupying lesions due to one of several potential causes ranging from brain tumors to hematomas.

Head trauma may cause cerebellar tonsillar ectopia, possibly because of dural strain. Additionally, ectopia may be present but asymptomatic until whiplash causes it to become symptomatic. Posterior fossa hypoplasia causes reduced cerebral and spinal compliance.

Currently, research is focusing on identifying the role of the genes on 18p in causing the signs and symptoms associated with deletions of 18p. This will ultimately enable predictive genotyping.

TGIF-Mutations and deletions of this gene have been associated with holoprosencephaly. Penetrance is incomplete, meaning that a deletion of one copy of this gene is not in and of itself sufficient to cause holoprosencephaly. Ten to fifteen percent of people with 18p- have holoprosencephaly, suggesting that other genetic and environmental facts play a role in the etiology of holoprosencephaly in these individuals.

Chiari malformations (CMs) are structural defects in the cerebellum. They consist of a downward displacement of the cerebellar tonsils through the foramen magnum (the opening at the base of the skull), sometimes causing non-communicating hydrocephalus as a result of obstruction of cerebrospinal fluid (CSF) outflow. The cerebrospinal fluid outflow is caused by phase difference in outflow and influx of blood in the vasculature of the brain. The malformation is named for Austrian pathologist Hans Chiari. A type II CM is also known as an Arnold–Chiari malformation in honor of Chiari and German pathologist Julius Arnold.

CMs can cause headaches, difficulty swallowing (sometimes accompanied by gagging), choking and vomiting, dizziness, nausea, neck pain, unsteady gait (problems with balance), poor hand coordination (fine motor skills), numbness and tingling of the hands and feet, and speech problems (such as hoarseness).

Less often, people with Chiari malformation may experience ringing or buzzing in the ears (tinnitus), weakness, slow heart rhythm, or fast heart rhythm, curvature of the spine (scoliosis) related to spinal cord impairment, abnormal breathing, such as central sleep apnea, characterized by periods of breathing cessation during sleep, and, in severe cases, paralysis.

Triploidy affects approximately 1-2% of pregnancies, but most miscarry early in development. At birth, males with triploidy are 1.5 times more common than females.

About 10-15% of individuals with 18p- have holoprosencephaly.

Approximately 10% of people with 18p- have a congenital heart anomaly. There does not appear to be a specific type of heart defect associated with a deletion of the short arm of chromosome 18. Septal defects, tetralogy of Fallot, dextrocardia, and coarctation of the aorta have all been reported in infants with 18p-.