The prevalence of congenital Chiari I malformation, defined as tonsilar herniations of 3 to 5 mm or greater, was previously believed to be in the range of one per 1000 births, but is likely much higher. Women are three times more likely than men to have a congenital Chiari malformation. Type II malformations are more prevalent in people of Celtic descent. A study using upright MRI found cerebellar tonsillar ectopia in 23% of adults with headache from motor-vehicle-accident head trauma. Upright MRI was more than twice as sensitive as standard MRI, likely because gravity affects cerebellar position.

Cases of congenital Chiari malformation may be explained by evolutionary and genetic factors. Typically, an infant's brain weighs around 400g at birth and triples to 1100-1400g by age 11. At the same time the cranium triples in volume from 500 cm to 1500 cm to accommodate the growing brain. During human evolution, the skull underwent numerous changes to accommodate the growing brain. The evolutionary changes included increased size and shape of the skull, decreased basal angle and basicranial length. These modifications resulted in significant reduction of the size of the posterior fossa in modern humans. In normal adults, the posterior fossa comprises 27% of the total intracranial space, while in adults with Chiari Type I, it is only 21%. If a modern brain is paired with a less modern skull, the posterior fossa may be too small, so that the only place where the cerebellum can expand is the foramen magnum, leading to development of Chiari Type I. H. neanderthalensis had platycephalic (flattened) skull. Some cases of Chiari are associated with platybasia (flattening of the skull base).

10-15% of intracranial AV malformations are DAVFs. There is a higher preponderance in females (61-66%), and typically patients are in their fourth or fifth generation of life. DAVFs are rarer in children.

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.

Arachnoid cysts are seen in up to 1.1% of the population with a gender distribution of 2:1 male:female Only 20% of these have symptoms, usually from secondary hydrocephalus.

A study that looked at 2,536 healthy young males found a prevalence of 1.7% (95% CI 1.2 to 2.3%). Only a small percentage of the detected abnormalities require urgent medical attention.

Environmental factors refer for example to maternal smoking and the maternal exposure to amine-containing drugs. Several research groups have found evidence that these environmental factors are responsible for an increase in the risk of craniosynostosis, likely through effects on fibroblast growth factor receptor genes.

On the other hand, a recent evaluation of valproic acid (an anti-epilepticum), which has been implicated as a causative agent, has shown no association with craniosynostosis.

Certain medication (like amine-containing drugs) can increase the risk of craniosynostosis when taken during pregnancy, these are so-called teratogenic factors.

Manual carotid self compression is a controversial treatment for DAVF. Patients using this method are told to compress the carotid with the opposite hand for approximately 10 minutes daily, and gradually increasing the frequency and duration of compression. Currently, it is unclear whether this method is an effective therapy.

Most arachnoid cysts are asymptomatic, and do not require treatment. Where complications are present, leaving arachnoid cysts untreated, may cause permanent severe neurological damage due to the progressive expansion of the cyst(s) or hemorrhage (bleeding). However, with treatment most individuals with symptomatic arachnoid cysts do well.

More specific prognoses are listed below:

- Patients with impaired preoperative cognition had postoperative improvement after surgical decompression of the cyst.

- Surgery can resolve psychiatric manifestations in selected cases.

Biomechanical factors include fetal head constraint during pregnancy. It has been found by Jacob et al. that constraint inside the womb is associated with decreased expression of Indian Hedgehog protein and noggin. These last two are both important factors influencing bone development.

Basilar invagination can be present at birth. If the condition develops after birth, it is usually the result of injury or diseases. If due to injury, about half the time it is caused by vehicle or bicycle accidents; 25% of the time by falls and 10% of the time by recreational activities such as diving accidents.

It also occurs in patients with bone diseases, such as osteomalacia, rheumatoid arthritis, Paget's disease, Ehlers-Danlos syndrome, Marfan syndrome, and osteogenesis imperfecta.

There has been a great deal of research to understand the cause of PHACE Syndrome. The abnormalities associated with this syndrome are thought to be due to errors that occur very early during development. Unfortunately, why the errors occur, or the exact cause is still unknown. PHACE has a shared biology of other vascular anomalies. There may be a genetic component involved and studies are underway to investigate this idea. No familial cases have been identified to date. Research is ongoing to find the cause of all vascular anomalies including PHACE Syndrome.

Imperforate anus has an estimated incidence of 1 in 5000 births. It affects boys and girls with similar frequency. However, imperforate anus will present as the low version 90% of the time in females and 50% of the time in males.

Imperforate anus is an occasional complication of sacrococcygeal teratoma.

The precise causes of syringomyelia are still unknown although blockage to the flow of cerebrospinal fluid has been known to be an important factor since the 1970s. Scientists in the UK and America continue to explore the mechanisms that lead to the formation of syrinxes in the spinal cord. It has been demonstrated a block to the free flow of cerebrospinal fluid is a contributory factor in the pathogenesis of the disease. Duke University in America and Warwick University are conducting research to explore genetic features of syringomyelia.

Surgical techniques are also being refined by the neurosurgical research community. Successful procedures expand the area around the cerebellum and spinal cord, thus improving the flow of cerebrospinal fluid thereby reducing the syrinx.

It is also important to understand the role of birth defects in the development of hindbrain malformations that can lead to syringomyelia as syringomyelia is a feature of intrauterine life and is also associated with spina bifida. Learning when these defects occur during the development of the fetus can help us understand this and similar disorders, and may lead to preventive treatment that can stop the formation of some birth abnormalities. Dietary supplements of folic acid prior to pregnancy have been found to reduce the number of cases of spina bifida and are also implicated in prevention of cleft palate and some cardiac defects.

Diagnostic technology is another area for continued research. MRI has enabled scientists to see conditions in the spine, including syringomyelia before symptoms appear. A new technology, known as dynamic MRI, allows investigators to view spinal fluid flow within the syrinx. CT scans allow physicians to see abnormalities in the brain, and other diagnostic tests have also improved greatly with the availability of new, non-toxic, contrast dyes.

Pectus malformations are common; about 1 in 400 people have a pectus disorder.

Pectus carinatum is rarer than pectus excavatum, another pectus disorder, occurring in only about 20% of people with pectus malformations. About four out of five patients are males.

After adolescence, some men and women use bodybuilding as a means to hide their malformation. Some women find that their breasts, if large enough, serve the same purpose. Some plastic surgeons perform breast augmentation to disguise mild to moderate cases in women. Bodybuilding is suggested for people with symmetrical pectus carinatum.

In a newborn boy thought to have Fryns syndrome, Clark and Fenner-Gonzales (1989) found mosaicism for a tandem duplication of 1q24-q31.2. They suggested that the gene for this disorder is located in that region. However, de Jong et al. (1989), Krassikoff and Sekhon (1990), and Dean et al. (1991) found possible Fryns syndrome associated with anomalies of chromosome 15, chromosome 6, chromosome 8(human)and chromosome 22, respectively. Thus, these cases may all represent mimics of the mendelian syndrome and have no significance as to the location of the gene for the recessive disorder.

By array CGH, Slavotinek et al. (2005) screened patients with DIH and additional phenotypic anomalies consistent with Fryns syndrome for cryptic chromosomal aberrations. They identified submicroscopic chromosome deletions in 3 probands who had previously been diagnosed with Fryns syndrome and had normal karyotyping with G-banded chromosome analysis. Two female infants were found to have microdeletions involving 15q26.2 (see 142340), and 1 male infant had a deletion in band 8p23.1 (see 222400).

In France, Aymé, "et al." (1989) estimated the prevalence of Fryns syndrome to be 0.7 per 10,000 births based on the diagnosis of 6 cases in a series of 112,276 consecutive births (live births and perinatal deaths).

In utero exposure to cocaine and other street drugs can lead to septo-optic dysplasia.

The first major form relates to an abnormality of the brain called an Arnold–Chiari malformation or Chiari Malformation. This is the most common cause of syringomyelia, where the anatomic abnormality, which may be due to a small posterior fossa, causes the lower part of the cerebellum to protrude from its normal location in the back of the head into the cervical or neck portion of the spinal canal. A syrinx may then develop in the cervical region of the spinal cord. Here, symptoms usually begin between the ages of 25 and 40 and may worsen with straining, called a valsalva maneuver, or any activity that causes cerebrospinal fluid pressure to fluctuate suddenly. Some patients, however, may have long periods of stability. Some patients with this form of the disorder also have hydrocephalus, in which cerebrospinal fluid accumulates in the skull, or a condition called arachnoiditis, in which a covering of the spinal cord—the arachnoid membrane—is inflamed.

Some cases of syringomyelia are familial, although this is rare.

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

Acute injury to the internal carotid artery (carotid dissection, occlusion, pseudoaneurysm formation) may be asymptomatic or result in life-threatening bleeding. They are almost exclusively observed when the carotid canal is fractured, although only a minority of carotid canal fractures result in vascular injury. Involvement of the petrous segment of the carotid canal is associated with a relatively high incidence of carotid injury.

The majority of patients with neurocutaneous melanosis are asymptomatic and therefore have a good prognosis with few complications. Most are not diagnosed, so definitive data in not available. For symptomatic patients, the prognosis is far worse. In patients without the presence of melanoma, more than 50% die within 3 years of displaying symptoms. While those with malignancy have a mortality rate of 77% with most patients displaying symptoms before the age of 2.

The presence of a Dandy-Walker malformation along with neurocutaneous melanosis, as occurs in 10% of symptomatic patients, further deteriorates prognosis. The median survival time for these patients is 6.5 months after becoming symptomatic.

Basilar invagination is invagination (infolding) of the base of the skull that occurs when the top of the C2 vertebra migrates upward. It can cause narrowing of the foramen magnum (the opening in the skull where the spinal cord passes through to the brain). It also may press on the lower brainstem.

This is similar to Chiari malformation. That, however, is usually present at birth.

PHACE Syndrome is the uncommon association between large infantile hemangiomas, usually of the face, and birth defects of the brain, heart, eyes, skin and/or arteries. It is an acronym that stands for the medical names of the parts of the body it often impacts:

- Posterior fossa abnormalities and other structural brain abnormalities

- Hemangioma(s) of the cervical facial region

- Arterial cerebrovascular anomalies

- Cardiac defects, aortic coarctation and other aortic abnormalities

- Eye anomalies

Sometimes an "S" is added to PHACE making the acronym PHACES; with the "S" standing for "Sternal defects" and/or "Supraumbilical raphe."

In 1993, an association between large facial hemangiomas and brain defects among 9 subjects was reported. 3 years later, a larger case study was published showing a wider spectrum of grouped malformations. The association of anomalies and the PHACES acronym was first coined by Dr. Vail Reese and Dr. Ilona Frieden in 1996, making it a newly described syndrome. A diagnosis is generally made from the physical examination, along with imaging of the head and chest, and an eye examination. PHACE is most commonly diagnosed among female infants. Long-term quality of life varies.

Hemangioma growth phase can last anywhere from 6 to 18 months. Then involution, or healing, of the hemangioma begins. Laser and other surgeries usually are able to make a substantial positive impact on appearance. Long after the hemangioma recedes, any damage it or the other defects caused, may remain. Migraines are common, as are developmental delays.

Rare familial recurrence has been reported, suggesting at least one genetic form (HESX1). In addition to HESX1, mutations in OTX2, SOX2 and PAX6 have been implicated in de Morsier syndrome, but in most cases SOD is a sporadic birth defect of unknown cause and does not recur with subsequent pregnancies.

Hemangioblastomas can cause polycythemia due to ectopic production of erythropoietin as a paraneoplastic syndrome.