It is still unknown which bio-chemical mechanisms lead to the occurrence of West syndrome. It is conjectured that it is a malfunction of neurotransmitter function, or more precisely, a malfunction in the regulation of the GABA transmission process. Another possibility being researched is a hyper-production of the Corticotropin-releasing hormone (CRH). It is possible that more than one factor is involved. Both hypotheses are supported by the effect of certain medications used to treat West syndrome.

Cases of epilepsy have been historically divided into three different groups: symptomatic, cryptogenic, and unknown. The International League Against Epilepsy (ILAE) recommended in 2011 to abandon these terms for reasons of clarity and instead try to place individual cases into one of the following 3 groups: genetic, structural/metabolic, and unknown. The new terms are more immediately clear in their meaning, except that the structural and metabolic group includes cases that have a genetic component that does not always directly lead to the condition. Only the genetic grouping has a known direct genetic cause. "Unknown" cases may be of "unknown" genetic, structural, metabolic, or other unknown cause.

The old terminology was defined by the ILAE as follows:

- symptomatic: the epilepsy is the consequence of a known or suspected disorder of the central nervous system.

- cryptogenic: this refers to a disorder whose cause is hidden or occult. Cryptogenic epilepsies are presumed to be symptomatic.

- idiopathic: there is no underlying cause other than a possible hereditary predisposition.

The remainder of this section will refer to the older terminology.

West syndrome appears in 1% to 5% of infants with Down syndrome. This form of epilepsy is relatively difficult to treat in children who do not have the chromosomal abnormalities involved in Down syndrome. However, in children with Down syndrome, the syndrome is often far more mild, and the children often react better to medication. The German Down Syndrom InfoCenter noted in 2003 that what was normally a serious epilepsy was in such cases often a relatively benign one.

EEG records for children with Down syndrome are often more symmetrical with fewer unusual findings. Although not all children can become entirely free from attacks with medication, children with Down syndrome are less likely to go on to develop Lennox-Gastaut syndrome or other forms of epilepsy than those without additional hereditary material on the 21st chromosome. The reason why it is easier to treat children with Down syndrome is not known.

If, however, a child with Down syndrome has seizures that are difficult to control, the child should be accessed for autistic spectrum disorder.

The prognosis varies widely from case to case, depending on the severity of the symptoms. However, almost all people reported with Aicardi syndrome to date have experienced developmental delay of a significant degree, typically resulting in mild to moderate to profound intellectual disability. The age range of the individuals reported with Aicardi syndrome is from birth to the mid 40s.

There is no cure for this syndrome.

Worldwide prevalence of Aicardi Syndrome is estimated at several thousand, with approximately 900 cases reported in the United States.

Nevo Syndrome is considered to be a rare disorder. Since its first appearance in 1974, only a handful of cases have been reported. Studies have shown showing similarities between Nevo Syndrome with Ehlers-Danlos syndrome as well as Sotos syndrome. There is an astounding overlap of phenotypic manifestations between Nevo Syndrome and the more frequent Sotos syndrome, which are both caused by the NSD1 deletion. Sotos syndrome is an autosomal dominant condition associated with learning disabilities, a distinctive facial appearance, and overgrowth. Studies have shown an overwhelming occurrence (half of those involved in the study) of Nevo syndrome in those individuals of Middle-Eastern descent.

Roberts syndrome is an extremely rare condition that only affects about 150 reported individuals. Although there have been only about 150 reported cases, the affected group is quite diverse and spread worldwide. Parental consanguinity (parents are closely related) is common with this genetic disorder. The frequency of Roberts syndrome carriers is unknown.

Perlman syndrome is a rare disease with an estimated incidence of less than 1 in 1,000,000. As of 2008, less than 30 patients had ever been reported in the world literature.

3C syndrome is very rare, occurring in less than 1 birth per million. Because of consanguinity due to a founder effect, it is much more common in a remote First Nations village in Manitoba, where 1 in 9 people carries the recessive gene.

Nevo Syndrome is an autosomal recessive disorder. Most times in which a child is afflicted with Nevo Syndrome, both their parents are of average height and weight. It is only until after birth when the characteristic physical traits associated with disease are manifested, and the disorder is actually diagnosed. One study showed that despite the increased growth rates, the patient was completely healthy up until age 6, when he was admitted into the hospital. Nevo syndrome is usually associated with early childhood fatality. Children with Nevo Syndrome have a high occurrence of death due to cardiac arrest because their developing hearts cannot keep up with their overgrown body.

Roberts syndrome, or sometimes called "pseudothalidomide syndrome", is an extremely rare genetic disorder that is characterized by mild to severe prenatal retardation or disruption of cell division, leading to malformation of the bones in the skull, face, arms, and legs.

Roberts syndrome is also known by many other names, including: hypomelia-hypotrichosis-facial hemangioma syndrome, SC syndrome (once thought to be an entirely separate disease), pseudothalidomide syndrome, Roberts-SC phocomelia syndrome, SC phocomelia syndrome, Appelt-Gerken-Lenz syndrome, RBS, SC pseudothalidomide syndrome, and tetraphocomelia-cleft palate syndrome. It is a genetic disorder caused by the mutation of the ESCO2 gene on 8th chromosome. Named after the famous Philadelphia surgeon and physician, Dr. John Bingham Roberts (1852–1924), who first described the syndrome in 1919, it is one of the rarest autosomal recessive disorders, affecting approximately 150 known individuals.

The syndrome is both autosomal, in that there are equal numbers of copies of the gene in both males and females, and recessive, meaning the child must inherit the defective gene from both parents. The mutation causes cell division to occur slowly or unevenly, and the cells with abnormal genetic content die. Roberts syndrome can affect both males and females. Although the disorder is rare, the affected group is diverse. The mortality rate is high in severely affected individuals.

As the syndrome is due to a chromosomal non-disjunction event, the recurrence risk is not high compared to the general population. There has been no evidence found that indicates non-disjunction occurs more often in a particular family.

It can be detected by the naked eye as well as dental or skull X-Ray testing.

Muenke syndrome is caused by a specific gene mutation in the FGFR3 gene. The mutation arises randomly; there is no full understanding for what causes this mutation. This mutation causes the FGFR3 protein to be overly active; it interferes with normal bone growth, and allows skull bones to fuse prematurely. There is no connection between anything mother did (or did not do) to activate the syndrome. If neither of the parents have Muenke syndrome, chances of having another child with the syndrome are minimal.

This condition is inherited in an autosomal dominant pattern. This means if a parent has Muenke syndrome, every newborn has a 50% chance of inheriting the syndrome.

While not always pathological, it can present as a birth defect in multiple syndromes including:

- Catel–Manzke syndrome

- Bloom syndrome

- Coffin–Lowry syndrome

- congenital rubella

- Cri du chat syndrome

- DiGeorge's syndrome

- Ehlers-Danlos syndrome

- fetal alcohol syndrome

- Hallermann-Streiff syndrome

- Hemifacial microsomia (as part of Goldenhar syndrome)

- Juvenile idiopathic arthritis

- Marfan syndrome

- Noonan syndrome

- Pierre Robin syndrome

- Prader–Willi syndrome

- Progeria

- Russell-Silver syndrome

- Seckel syndrome

- Smith-Lemli-Opitz syndrome

- Treacher Collins syndrome

- Trisomy 13 (Patau syndrome)

- Trisomy 18 (Edwards syndrome)

- Wolf–Hirschhorn syndrome

- X0 syndrome (Turner syndrome)

Prognoses for 3C syndrome vary widely based on the specific constellation of symptoms seen in an individual. Typically, the gravity of the prognosis correlates with the severity of the cardiac abnormalities. For children with less severe cardiac abnormalities, the developmental prognosis depends on the cerebellar abnormalities that are present. Severe cerebellar hypoplasia is associated with growth and speech delays, as well as hypotonia and general growth deficiencies.

In mild cases, individuals with XXXY syndrome may lead a relatively good life. These individuals may face difficulties in communicating with others due to their language-based deficits. These deficits may make forming bonds with others difficult, but fulfilling relationships with others are still achievable. Those with higher scores in adaptive functioning are likely to have higher quality of life because they can be independent.

Many of the congenital malformations found with Malpuech syndrome can be corrected surgically. These include cleft lip and palate, omphalocele, urogenital and craniofacial abnormalities, skeletal deformities such as a caudal appendage or scoliosis, and hernias of the umbillicus. The primary area of concern for these procedures applied to a neonate with congenital disorders including Malpuech syndrome regards the logistics of anesthesia. Methods like tracheal intubation for management of the airway during general anesthesia can be hampered by the even smaller, or maldeveloped mouth of the infant. For regional anesthesia, methods like spinal blocking are more difficult where scoliosis is present. In a 2010 report by Kiernan et al., a four-year-old girl with Malpuech syndrome was being prepared for an unrelated tonsillectomy and adenoidectomy. While undergoing intubation, insertion of a laryngoscope, needed to identify the airway for the placement of the endotracheal tube, was made troublesome by the presence of micrognathia attributed to the syndrome. After replacement with a laryngoscope of adjusted size, intubation proceeded normally. Successful general anesthesia followed.

A rare follow-up of a male with Malpuech syndrome was presented by Priolo et al. (2007). Born at term from an uneventful pregnancy and delivery, the infant underwent a surgical repair of a cleft lip and palate. No problems were reported with the procedure. A heart abnormality, atrial septal defect, was also apparent but required no intervention. At age three years, mental retardation, hyperactivity and obsessive compulsive disorder were diagnosed; hearing impairment was diagnosed at age six, managed with the use of hearing aids. Over the course of the decade that followed, a number of psychiatric evaluations were performed. At age 14, he exhibited a fear of physical contact; at age 15, he experienced a severe psychotic episode, characterized by agitation and a loss of sociosexual inhibition. This array of symptoms were treated pharmocologically (with prescription medications). He maintained a low level of mental deficiency by age 17, with moments of compulsive echolalia.

Muenke syndrome is inherited in an autosomal dominant pattern. In some cases, an affected person inherits the mutation from one affected parent. If a patient is shown to have Muenke, they have a 50/50 chance of passing it on to their children. Not all cases of Muenke however is obvious. Other cases may result from new mutations in the gene. These cases occur in people with no history of the disorder in their family.

A single mutation in the FGFR3 gene cause this syndrome. The FGFR3 gene provides instructions for making a protein that is involved in the development and maintenance of bone and brain tissue. This mutation causes the FGFR3 protein to be overly active, which interferes with normal bone growth and allows the bones of the skull to fuse before they should.

As stated by researchers at the University of Washington, Muenke syndrome is inherited in an autosomal dominant manner with incomplete penetrance and variable expressivity.” Prenatal diagnosis for pregnancies at increased risk is possible if the defining mutation has been identified in the family (Agochukwu et.al. 2006). According to the article "Craniosynostosis: Molecular Genetics," penetrance is higher in females (87%) than in males (76%). Muenke syndrome is estimated to account for 25%-30% of all genetic causes of craniosynostosis according to the Journal of Anatomy.

The Kocher–Debré–Semelaigne syndrome is hypothyroidism in infancy or childhood characterised by lower extremity or generalized muscular hypertrophy, myxoedema, short stature and cretinism. The absence of painful spasms and pseudomyotonia differentiates this syndrome from its adult form, which is Hoffmann syndrome.

The syndrome is named after Emil Theodor Kocher, Robert Debré and Georges Semelaigne.

Also known as Debre–Semelaigne syndrome or cretinism-muscular hypertrophy, hypothyroid myopathy, hypothyroidism-large muscle syndrome, hypothyreotic muscular hypertrophy in children, infantile myxoedema-muscular hypertrophy, myopathy-myxoedema syndrome, myxoedema-muscular hypertrophy syndrome, myxoedema-myotonic dystrophy syndrome.

Kocher-Debre-Semelaigne syndrome gives infant a Hercules appearance.

The prognosis for patients diagnosed with Timothy syndrome is very poor. Of 17 children analyzed in one study, 10 died at an average age of 2.5 years. Of those that did survive, 3 were diagnosed with autism, one with an autism spectrum disorder, and the last had severe delays in language development. One patient with atypical Timothy syndrome was largely normal with the exception of heart arrhythmia. Likewise, the mother of two Timothy syndrome patients also carried the mutation but lacked any obvious phenotype. In both of these cases, however, the lack of severity of the disorder was due to mosaicism.

Pisa syndrome is predominantly caused by a prolonged administration or an overly dosed administration of antipsychotic drugs. Although antipsychotic drugs are known to be the main drugs that are concerned with this syndrome, several other drugs are reported to have caused the syndrome as well. Certain antidepressants, psychoactive drugs, and antiemetics have also been found to cause Pisa syndrome in patients.

Drugs found to have caused Pisa Syndrome:

- Atypical antipsychotic drugs- ex. clozapine, aripiprazole

- Tricyclic antidepressants- ex. clomipramine

- Psychoactive drugs

- Antiemetic drugs

- Cholinesterase inhibitors

- Galantamine

Based on the drugs that caused Pisa syndrome, it has been implicated that the syndrome may be due to a dopaminergic-cholinergic imbalance or a serotonergic or noradrenergic dysfunction. For the development of Pisa syndrome that cannot be alleviated by anticholinergic drugs, it has been considered that asymmetric brain functions or neural transmission may be the underlying mechanism. How these drugs interact with the biochemistry of the brain to cause the syndrome is unknown and a topic of current research.

More than 80% of children with Patau syndrome die within the first year of life. Children with the mosaic variation are usually affected to a lesser extent. In a retrospective Canadian study of 174 children with trisomy 13, median survival time was 12.5 days. One and ten year survival was 19.8% and 12.9% respectively.

The incidence of Fraser syndrome is 0.043 per 10,000 live born infants and 1.1 in 10,000 stillbirths, making it a rare syndrome.

Anticholinergic drugs have been reported to be extremely effective in 40% of the patients with the Pisa syndrome. Patients with Pisa syndrome that is resistant to anticholinergic drugs is mostly resolved by the reduction of the administration of the antipsychotic drugs as previously mentioned. While the specific pathology underlying idiopathic Pisa syndrome is unknown, the administration of anticholinergic drugs has provided resolution in known cases.

Because oculocerebrorenal syndrome is an X-linked recessive condition, the disease develops mostly in men with very rare occurrences in women, while women are carriers of the disease; it has an estimated prevalence of 1 in 500,000 people. Boys with Lowe syndrome are born with cataracts in both eyes, glaucoma is present in about half of the individuals with Lowe syndrome, though usually not at birth. While not present at birth, many affected boys develop kidney problems at about one year of age. Renal pathology is characterized by an abnormal loss of certain substances into the urine, including bicarbonate, sodium, potassium, amino acids, organic acids, albumin, calcium and L-carnitine, this problem, is known as Fanconi-type renal tubular dysfunction.