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.

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).

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%.

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.

Cervical stenosis may be present from birth or may be caused by other factors:

- Surgical procedures performed on the cervix such as colposcopy, cone biopsy, or a cryosurgery procedure

- Trauma to the cervix

- Repeated vaginal infections

- Atrophy of the cervix after menopause

- Cervical cancer

- Radiation

- Cervical nabothian cysts

When Tarlov cysts are ruptured or drained they cause leakage of cerebrospinal fluid (CSF). Ruptures of Tarlov cysts have been reported associated with communicating aneurysms and from fracture in the proximity of the cysts. An undetected rupture can cause intracranial hypotension, including orthostatic neurological symptoms along with headache, nausea, and vomiting that improve when supine. The ruptured cysts can be patched either with a biosynthetic dural patch or using a blood patch to stem the flow of CSF.

A genetic disorder called “Brickers-Adams-Edwards syndrome” or “X-linked hydrocephalus” has been discovered that leads to aqueductal stenosis. This disease is transmitted from mother to son. This disorder is caused by a point mutation in the gene for neural cell adhesion. Most males born with this have severe hydrocephalus, adducted thumbs, spastic motions, and intellectual problems. Females with this defect may have adducted thumbs or subnormal intelligence.

Bacterial meningitis can also result in gliotic blockage of the aqueduct. In utero infection or infection during infancy could both result in glial cell build up to make an obstruction.

Cervical stenosis may impact natural fertility by impeding the passage of semen into the uterus. In the context of infertility treatments, cervical stenosis may complicate or prevent the use of intrauterine insemination (IUI) or in vitro fertilization (IVF) procedures.

Diastematomyelia (occasionally diastomyelia) is a congenital disorder in which a part of the spinal cord is split, usually at the level of the upper lumbar vertebra.

Diastematomyelia is a rare congenital anomaly that results in the "splitting" of the spinal cord in a longitudinal (sagittal) direction. Females are affected much more commonly than males. This condition occurs in the presence of an osseous (bone), cartilaginous or fibrous septum in the central portion of the spinal canal which then produces a complete or incomplete sagittal division of the spinal cord into two hemicords. When the split does not reunite distally to the spur, the condition is referred to as a diplomyelia, or true duplication of the spinal cord.

Subglottic stenosis is a congenital or acquired narrowing of the subglottic airway. Although it is relatively rare, it is the third most common congenital airway problem (after laryngomalacia and vocal cord paralysis). Subglottic stenosis can present as a life-threatening airway emergency. It is imperative that the otolaryngologist be an expert at dealing with the diagnosis and management of this disorder. Subglottic stenosis can affect both children and adults.

Subglottic stenosis can be of three forms, namely congenital subglottic stenosis, idiopathic subglottic stenosis (ISS) and acquired subglottic stenosis. As the name suggests, congenital subglottic stenosis is a birth defect. Idiopathic subglottic stenosis is a narrowing of the airway due to an unknown cause. Acquired subglottic stenosis generally follows as an after-effect of airway intubation, and in extremely rare cases as a result of gastroesophageal reflux disease (GERD).

Subglottic stenosis is graded according to the Cotton-Meyer classification system from one to four based on the severity of the blockage.

Grade 1 – <50% obstruction

Grade 2 – 51–70% obstruction

Grade 3 – 71–99% obstruction

Grade 4 – no detectable lumen

Treatments to alleviate the symptoms of subglottic stenosis includes a daily dose of steroids such as prednisone, which reduces the inflammation of the area for better breathing. Other medications such as Methotrexate is also being tested by patients but results are pending.

Tarlov cysts are known to have the tendency to enlarge over time. The prominent theory that explains this phenomenon reasons the enlargement of the cysts is due to the cerebrospinal fluid being pushed into the cyst during systole pulsation, but unable to get out during the diastole phase, resulting in enlargement observed in clinical settings over time. Increased ICP from trauma or other injury, childbirth, and overextertion are thought to trigger enlargement along with inflammation and hemorrhagic infiltration. With the cysts often containing a valve like mechanism fluid becomes trapped, and the meningeal sac or nerve sheath grows in size. Some patients have been diagnosed for up to 20 years with little change in size, and those with small stable cysts may avoid much progression of symptoms. Those with generally larger sacral cysts pressed along the sacrum cause the sacrum to become eroded and thin.

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.

Atresia is a condition in which an orifice or passage in the body is (usually abnormally) closed or absent.

Examples of atresia include:

- Biliary atresia, a condition in newborns in which the common bile duct between the liver and the small intestine is blocked or absent.

- Choanal atresia, blockage of the back of the nasal passage, usually by abnormal bony or soft tissue.

- Esophageal atresia, which affects the alimentary tract and causes the esophagus to end before connecting normally to the stomach.

- Imperforate anus, malformation of the opening between the rectum and anus.

- Intestinal atresia, malformation of the intestine, usually resulting from a vascular accident in utero.

- Microtia, absence of the ear canal or failure of the canal to be tubular or fully formed (can be related to Microtia, a congenital deformity of the pinna, or outer ear).

- Ovarian follicle atresia, the degeneration and subsequent resorption of one or more immature ovarian follicles.

- Potter sequence, congenital decreased size of the kidney leading to absolutely no functionality of the kidney, usually related to a single kidney.

- Pulmonary atresia, malformation of the pulmonary valve in which the valve orifice fails to develop.

- Renal agenesis, only having one kidney.

- Tricuspid atresia, a form of congenital heart disease whereby there is a complete absence of the tricuspid valve, and consequently an absence of the right atrioventricular connection.

- Vaginal atresia, a congenital occlusion of the vagina or subsequent adhesion of the walls of the vagina, resulting in its occlusion.

Generally, there are two forms of syringomyelia: congenital and acquired. (In addition, one form of the disorder involves the brainstem. The brainstem controls many of our vital functions, such as respiration and heartbeat. When syrinxes affect the brainstem, the condition is called syringobulbia.)

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.

Vertebral anomalies is associated with an increased incidence of some other specific anomalies as well, together being called the VACTERL association:

- V - "Vertebral anomalies"

- A - Anal atresia

- C - Cardiovascular anomalies

- T - Tracheoesophageal fistula

- E - Esophageal atresia

- R - Renal (Kidney) and/or radial anomalies

- L - Limb defects

Most people with mild to moderate symptoms do not get worse. While many improve in the short term after surgery this improvement decreases somewhat with time. A number of factors present before surgery are able to predict the outcome after surgery, with people with depression, cardiovascular disease and scoliosis doing in general worse while those with more severe stenosis beforehand and better overall health doing better.

The natural evolution of disc disease and degeneration leads to stiffening of the intervertebral joint. This leads to osteophyte formation—a bony overgrowth about the joint. This process is called spondylosis, and is part of the normal aging of the spine. This has been seen in studies of normal and diseased spines. Degenerative changes begin to occur without symptoms as early as age 25–30 years. It is not uncommon for people to experience at least one severe case of low back pain by the age of 35 years. This can be expected to improve and become less prevalent as the individual develops osteophyte formation around the discs.

In the US workers' compensation system, once the threshold of two major spinal surgeries is reached, the vast majority of workers will never return to any form of gainful employment. Beyond two spinal surgeries, any more are likely to make the patient worse, not better.

Surgery

Surgical intervention is warranted in patients who present with new onset neurological signs and symptoms or have a history of progressive neurological manifestations which can be related to this abnormality. The surgical procedure required for the effective treatment of diastematomyelia includes decompression (surgery) of neural elements and removal of bony spur. This may be accomplished with or without resection and repair of the duplicated dural sacs. Resection and repair of the duplicated dural sacs is preferred since the dural abnormality may partly contribute to the "tethering" process responsible for the symptoms of this condition.

Post-myelographic CT scanning provides individualized detailed maps that enable surgical treatment of cervical diastematomyelia, first performed in 1983.

Observation

Asymptomatic patients do not require surgical treatment. These patients should have regular neurological examinations since it is known that the condition can deteriorate. If any progression is identified, then a resection should be performed.

In cases of aqueductal stenosis caused by tumor compression, a brain tumor in the region of the midbrain forms. More specific anatomically, a tumor forms in the pineal region which is dorsal to the midbrain and is level with the aqueduct of Sylvius. As the tumor grows and expands, it compresses the aqueduct to eventually obstruct it.

Cervical spinal stenosis is a bone disease involving the narrowing of the spinal canal at the level of the neck. It is frequently due to chronic degeneration, but may also be congenital. Treatment is frequently surgical.

Cervical spinal stenosis is one of the most common forms of spinal stenosis, along with lumbar spinal stenosis (which occurs at the level of the lower back instead of in the neck). Thoracic spinal stenosis, at the level of the mid-back, is much less common. Cervical spinal stenosis can be far more dangerous by compressing the spinal cord. Cervical canal stenosis may lead to serious symptoms such as major body weakness and paralysis. Such severe spinal stenosis symptoms are virtually absent in lumbar stenosis, however, as the spinal cord terminates at the top end of the adult lumbar spine, with only nerve roots (cauda equina) continuing further down. Cervical spinal stenosis is a condition involving narrowing of the spinal canal at the level of the neck. It is frequently due to chronic degeneration, but may also be congenital or traumatic. Treatment frequently is surgical.

Congenital vertebral anomalies are a collection of malformations of the spine. Most around 85% are not clinically significant, but they can cause compression of the spinal cord by deforming the vertebral canal or causing instability. This condition occurs in the womb. Congenital vertebral anomalies include alterations of the shape and number of vertebrae.

Tethered spinal cord can be caused by various conditions but the main cause is when tissue attachments limit the movement of the spinal cord in the spinal column which causes abnormal stretching of the cord. The tethered spinal cord syndrome is correlated with having the causes:

- Spina bifida

- Occulta

- Mylomeningocele

- Meningocele

- History of spinal trauma

- History of spinal surgery

- Tumor(s) in the spinal column

- Thickened and/or tight filum terminale

- Lipoma(s) in the spinal column

- Dermal Sinus Tract (congenital deformity)

- Diastematomyelia (split spinal cord)

Tethered spinal cord is a disorder and not a mechanism so it does not spread to other people and there are no measures that can be done to prevent it beforehand. The only preventative measure that is successful is to surgically untether the spinal cord though there might already be irreversible damage.

The most common forms are cervical spinal stenosis, which are at the level of the neck, and lumbar spinal stenosis, at the level of the lower back. Thoracic spinal stenosis, at the level of the mid-back, is much less common.

In lumbar stenosis, the spinal nerve roots in the lower back are compressed which can lead to symptoms of sciatica (tingling, weakness, or numbness that radiates from the low back and into the buttocks and legs).

Cervical spinal stenosis can be far more dangerous by compressing the spinal cord. Cervical canal stenosis may lead to myelopathy, a serious conditions causing symptoms including major body weakness and paralysis. Such severe spinal stenosis symptoms are virtually absent in lumbar stenosis, however, as the spinal cord terminates at the top end of the adult lumbar spine, with only nerve roots (cauda equina) continuing further down. Cervical spinal stenosis is a condition involving narrowing of the spinal canal at the level of the neck. It is frequently due to chronic degeneration, but may also be congenital or traumatic. Treatment frequently is surgical.

99% of cervical polyps will remain benign and 1% will at some point show neoplastic change. Cervical polyps are unlikely to regrow.