Systemic infections can result in neurodevelopmental consequences, when they occur in infancy and childhood of humans, but would not be called a primary neurodevelopmental disorder per se, as for example HIV Infections of the head and brain, like brain abscesses, meningitis or encephalitis have a high risk of causing neurodevelopmental problems and eventually a disorder. For example, measles can progress to subacute sclerosing panencephalitis.

A number of infectious diseases can be transmitted either congenitally (before or at birth), and can cause serious neurodevelopmental problems, as for example the viruses HSV, CMV, rubella (congenital rubella syndrome), Zika virus, or bacteria like "Treponema pallidum" in congenital syphilis, which may progress to neurosyphilis if it remains untreated. Protozoa like "Plasmodium" or "Toxoplasma" which can cause congenital toxoplasmosis with multiple cysts in the brain and other organs, leading to a variety of neurological deficits.

Some cases of schizophrenia may be related to congenital infections though the majority are of unknown causes.

Nutrition disorders and nutritional deficits may cause neurodevelopmental disorders, such as spina bifida, and the rarely occurring anencephaly, both of which are neural tube defects with malformation and dysfunction of the nervous system and its supporting structures, leading to serious physical disability and emotional sequelae. The most common nutritional cause of neural tube defects is folic acid deficiency in the mother, a B vitamin usually found in fruits, vegetables, whole grains, and milk products. (Neural tube defects are also caused by medications and other environmental causes, many of which interfere with folate metabolism, thus they are considered to have multifactorial causes.) Another deficiency, iodine deficiency, produces a spectrum of neurodevelopmental disorders ranging from mild emotional disturbance to severe mental retardation. (see also cretinism)

Excesses in both maternal and infant diets may cause disorders as well, with foods or food supplements proving toxic in large amounts. For instance in 1973 K.L. Jones and D.W. Smith of the University of Washington Medical School in Seattle found a pattern of "craniofacial, limb, and cardiovascular defects associated with prenatal onset growth deficiency and developmental delay" in children of alcoholic mothers, now called fetal alcohol syndrome, It has significant symptom overlap with several other entirely unrelated neurodevelopmental disorders. It has been discovered that iron supplementation in baby formula can be linked to lowered I.Q. and other neurodevelopmental delays.

Among children, the cause of intellectual disability is unknown for one-third to one-half of cases. About 5% of cases are inherited from a person's parents. Genetic defects that cause intellectual disability but are not inherited can be caused by accidents or mutations in genetic development. Examples of such accidents are development of an extra chromosome 18 (trisomy 18) and Down syndrome, which is the most common genetic cause. Velocariofacial syndrome and fetal alcohol spectrum disorders are the two next most common causes. However, doctors have found many other causes. The most common are:

- Genetic conditions. Sometimes disability is caused by abnormal genes inherited from parents, errors when genes combine, or other reasons. The most prevalent genetic conditions include Down syndrome, Klinefelter syndrome, Fragile X syndrome (common among boys), neurofibromatosis, congenital hypothyroidism, Williams syndrome, phenylketonuria (PKU), and Prader–Willi syndrome. Other genetic conditions include Phelan-McDermid syndrome (22q13del), Mowat–Wilson syndrome, genetic ciliopathy, and Siderius type X-linked intellectual disability () as caused by mutations in the "PHF8" gene (). In the rarest of cases, abnormalities with the X or Y chromosome may also cause disability. 48, XXXX and 49, XXXXX syndrome affect a small number of girls worldwide, while boys may be affected by 49, XXXXY, or 49, XYYYY. 47, XYY is not associated with significantly lowered IQ though affected individuals may have slightly lower IQs than non-affected siblings on average.

- Problems during pregnancy. Intellectual disability can result when the fetus does not develop properly. For example, there may be a problem with the way the fetus' cells divide as it grows. A pregnant person who drinks alcohol (see fetal alcohol spectrum disorder) or gets an infection like rubella during pregnancy may also have a baby with intellectual disability.

- Problems at birth. If a baby has problems during labor and birth, such as not getting enough oxygen, he or she may have developmental disability due to brain damage.

- Exposure to certain types of disease or toxins. Diseases like whooping cough, measles, or meningitis can cause intellectual disability if medical care is delayed or inadequate. Exposure to poisons like lead or mercury may also affect mental ability.

- Iodine deficiency, affecting approximately 2 billion people worldwide, is the leading preventable cause of intellectual disability in areas of the developing world where iodine deficiency is endemic. Iodine deficiency also causes goiter, an enlargement of the thyroid gland. More common than full-fledged cretinism, as intellectual disability caused by severe iodine deficiency is called, is mild impairment of intelligence. Certain areas of the world due to natural deficiency and governmental inaction are severely affected. India is the most outstanding, with 500 million suffering from deficiency, 54 million from goiter, and 2 million from cretinism. Among other nations affected by iodine deficiency, China and Kazakhstan have instituted widespread iodization programs, whereas, as of 2006, Russia had not.

- Malnutrition is a common cause of reduced intelligence in parts of the world affected by famine, such as Ethiopia.

- Absence of the arcuate fasciculus.

Intellectual disability affects about 2–3% of the general population. 75–90% of the affected people have mild intellectual disability. Non-syndromic or idiopathic ID accounts for 30–50% of cases. About a quarter of cases are caused by a genetic disorder. Cases of unknown cause affect about 95 million people as of 2013.

Micro syndrome also known as WARBM, and Warburg–Sjo–Fledelius syndrome, is a rare autosomal recessive genetic disorder characterized by microcephaly, microcornea, congenital cataract, intellectual or developmental disability, optic atrophy, and hypogenitalism.

The syndrome primarily affects young males. Preliminary studies suggest that prevalence may be 1.8 per 10,000 live male births. 50% of those affected do not live beyond 25 years of age, with deaths attributed to the impaired immune function.

The rare cases that have been examined are often within families, or the people that have cases of micro syndrome have a mutation in their genes.

It can be associated with "RAB3GAP".

Global developmental delay is an umbrella term used when children are significantly delayed in their cognitive and physical development. There is usually a more specific condition which causes this delay, such as Fragile X syndrome or other chromosonal abnormalities. However, it is sometimes difficult to identify this underlying condition.

Other terms associated with this condition are failure to thrive (which focuses on lack of weight gain and physical development), intellectual disability (which focuses on intellectual deficits and the changes they cause to development) and developmental disability (which can refer to both intellectual and physical disability altering development).

Say–Neger syndrome is a rare X-linked genetic disorder that is mostly characterized as developmental delay. It is one of the rare causes of short stature. It is closely related with trigonocephaly (a misshapen forehead due to premature fusion of bones in the skull). People with Say–Meyer syndrome have impaired growth, deficits in motor skills development and mental state.

It is suggested that it is from a X-linked transmission.

Lujan–Fryns syndrome is a rare X-linked dominant syndrome, and is therefore more common in males than females. Its prevalence within the general population has not yet been determined.

Alopecia contractures dwarfism mental retardation syndrome or (ACD mental retardation syndrome) is a developmental disorder which causes mainly baldness and dwarfism in combination with intellectual disability; skeletal anomalies, caries and nearsightedness are also typical.

The ACD mental retardation syndrome was first described in 1980 by Albert Schinzel and only few cases have since been identified in the world. At the time Dr. Schinzel made no conclusion of the hereditary pattern of this syndrome but similarities between cases reported by year 2000 seem to suggest autosomal or x-linked recessive inheritance or possibly a dominant mutation caused by mosaicism as causes of this syndrome.

There are no objectively definitive statistics about how many people have savant skills. The estimates range from "exceedingly rare" to one in ten people with autism having savant skills in varying degrees. A 2009 British study of 137 parents of autistic children found that 28% believe their children met the criteria for a savant skill, defined as a skill or power "at a level that would be unusual even for 'normal' people". As many as 50 cases of sudden or acquired savant syndrome have been reported.

Males with savant syndrome outnumber females by roughly 6:1, slightly higher than the sex ratio disparity for autism spectrum disorders of 4.3:1.

Savant syndrome is a condition in which a person demonstrates one or more profound and prodigious capacities or abilities far in excess of what would be considered normal, yet often also has significant deficits in other areas of brain processing.

People with savant syndrome may have neurodevelopmental disorders, notably autism spectrum disorders (in which case they are often referred to as autistic savants), or brain injuries. The most dramatic examples of savant syndrome occur in individuals who score very low on IQ tests, while demonstrating exceptional skills or brilliance in specific areas, such as rapid calculation (hypercalculia), art, memory, or musical ability. Although termed a syndrome, it is not recognized as a mental disorder nor as part of a mental disorder in medical manuals such as the ICD-10 or the DSM-5.

Another form of savant syndrome is acquired savant syndrome, in which a person acquires prodigious capabilities or skills following dementia, a head injury or concussion, epilepsy, or other brain disturbances. This syndrome is more rare, with a study by Darold Treffert in 2010 showing that in a registry of 319 known savants, only 32 had acquired savant syndrome.

The growth retardation dates from the intrauterine period (development in the uterus.) The long-term developmental growth and outcome is not known, but the early childhood development is known, which is said to be moderately delayed. Craniosynostosis is usually rare among the X-Linked Intellectual Disability Syndromes, but when it is present, it affects the metopic structure (forehead).

Borderline intellectual functioning, also called borderline mental disability, is a categorization of intelligence wherein a person has below average cognitive ability (generally an IQ of 70–85), but the deficit is not as severe as intellectual disability (below 70). It is sometimes called below average IQ (BAIQ). This is technically a cognitive impairment; however, this group may not be sufficiently mentally disabled to be eligible for specialized services. The DSM-IV-TR codes borderline intellectual functioning as V62.89.

During school years, individuals with borderline intellectual functioning are often "slow learners." Although a large percentage of this group fails to complete high school and can often achieve only a low socioeconomic status, most adults in this group blend in with the rest of the population.

Genitopatellar Syndrome is an autosomal dominant inheritance where the mutation in the KAT6B causes the syndrome. The KAT6B gene is responsible for making an enzyme called histone acetyltransferase which functions in regulating and making of histone which are proteins that attach to DNA and give the chromosomes their shape. The function of histone acetyltransferase produced from KAT6B is unknown but it is considered as a regulator of early developments. There is little known about how the mutation in the KAT6B causes the syndrome but researchers suspects that the mutations occur near the end of the KAT6B gene and causes it to produce shortened acetyltransferase enzyme. The shortened enzyme alters the regulation of other genes. On the other hand, the mutation of KAT6B leading to the specific features of genitopatellar syndrome is still not surely proven.

Renpenning's syndrome is a neurodevelopmental disorder recognised in males that causes intellectual disability, mild growth retardation with examples in the testes and head, and a somewhat short stature. The condition only affects males, starting at birth, and was first characterized in 1962. but first described by Hans Renpenning in 1963 after he documented these traits on many children in one family alone.

It can be associated with "PQBP1".

Affected individuals have a somewhat shortened lifespan. The maximum described lifespan is 67 years. Adults with 13q deletion syndrome often need support services to maintain their activities of daily living, including adult day care services or housing services.

Overactive disorder associated with mental retardation and stereotyped movements is a pervasive developmental disorder (PDD) listed in Chapter V(F) of the tenth revision of the International Statistical Classification of Diseases and Related Health Problems (ICD-10); its diagnostic code is F84.4.

X-linked intellectual disability (previously known as X-linked mental retardation) refers to forms of intellectual disability which are specifically associated with X-linked recessive inheritance.

As with most X-linked disorders, males are more heavily affected than females. Females with one affected X chromosome and one normal X chromosome tend to have milder symptoms.

Unlike many other types of intellectual disability, the genetics of these conditions are relatively well understood. It has been estimated there are ~200 genes involved in this syndrome; of these ~100 have been identified.

X-linked intellectual disability accounts for ~16% of all cases of intellectual disability in males.

Intellectual disability in children can be caused by genetic or environmental factors. The individual could have a natural brain malformation or pre or postnatal damage done to the brain caused by drowning or a traumatic brain injury, for example. Nearly 30 to 50% of individuals with intellectual disability will never know the cause of their diagnosis even after thorough investigation.

Prenatal causes of intellectual disability include:

- Congenital infections such as cytomegalovirus, toxoplasmosis, herpes, syphilis, rubella and human immunodeficiency virus

- Prolonged maternal fever in the first trimester

- Exposure to anticonvulsants or alcohol

- Untreated maternal phenylketonuria (PKU)

- Complications of prematurity, especially in extremely low-birth-weight infants

- Postnatal exposure to lead

Single-gene disorders that result in intellectual disability include:

- Fragile X syndrome

- Neurofibromatosis

- Tuberous sclerosis

- Noonan's syndrome

- Cornelia de Lange's syndrome

These single-gene disorders are usually associated with atypical physical characteristics.

About 1/4 of individuals with intellectual disability have a detectable chromosomal abnormality. Others may have small amounts of deletion or duplication of chromosomes, which may go unnoticed and therefore, undetermined.

M2DS is one of the several types of X-linked intellectual disability. The cause of M2DS is a duplication of the MECP2 or Methyl CpG binding protein 2 gene located on the X chromosome (Xq28). The MeCP2 protein plays a pivotal role in regulating brain function. Increased levels of MECP2 protein results in abnormal neural function and impaired immune system. Mutations in the MECP2 gene are also commonly associated with Rett syndrome in females. Advances in genetic testing and more widespread use of Array Comparative Genomic Hybridization has led to increased diagnosis of MECP2 duplication syndrome. It is thought to represent ~1% of X-linked male mental disability cases.

Learning disability is a classification that includes several areas of functioning in which a person has difficulty learning in a typical manner, usually caused by an unknown factor or factors. Given the "difficulty learning in a typical manner", this does not exclude the ability to learn in a different manner. Therefore, some people can be more accurately described as having a "Learning Difference", thus avoiding any misconception of being disabled with a lack of ability to learn and possible negative stereotyping.

In the UK, the term "learning disability" generally refers to an intellectual disability, while difficulties such as dyslexia and dyspraxia are usually referred to as "learning difficulties".

While "learning disability, learning disorder" and "learning difficulty" are often used interchangeably, they differ in many ways. Disorder refers to significant learning problems in an academic area. These problems, however, are not enough to warrant an official diagnosis. Learning disability, on the other hand, is an official clinical diagnosis, whereby the individual meets certain criteria, as determined by a professional (psychologist, pediatrician, etc.). The difference is in degree, frequency, and intensity of reported symptoms and problems, and thus the two should not be confused. When the term "learning disorder" is used, it describes a group of disorders characterized by inadequate development of specific academic, language, and speech skills. Types of learning disorders include reading (dyslexia), mathematics (dyscalculia) and writing (dysgraphia).

The unknown factor is the disorder that affects the brain's ability to receive and process information. This disorder can make it problematic for a person to learn as quickly or in the same way as someone who is not affected by a learning disability. People with a learning disability have trouble performing specific types of skills or completing tasks if left to figure things out by themselves or if taught in conventional ways.

Individuals with learning disabilities can face unique challenges that are often pervasive throughout the lifespan. Depending on the type and severity of the disability, interventions, and current technologies may be used to help the individual learn strategies that will foster future success. Some interventions can be quite simplistic, while others are intricate and complex. Current technologies may require student training to be effective classroom supports. Teachers, parents, and schools can create plans together that tailor intervention and accommodations to aid the individuals in successfully becoming independent learners. School psychologists and other qualified professionals quite often help design the intervention and coordinate the execution of the intervention with teachers and parents.

Several X-linked syndromes include intellectual disability as part of the presentation. These include:

- Coffin–Lowry syndrome

- MASA syndrome

- MECP2 duplication syndrome

- X-linked alpha thalassemia mental retardation syndrome

- mental retardation and microcephaly with pontine and cerebellar hypoplasia

Weaver syndrome (also called Weaver-Smith syndrome) is an extremely rare congenital disorder associated with rapid growth beginning in the prenatal period and continuing through the toddler and youth years. It is characterized by advanced osseous maturation, and distinctive craniofacial, skeletal, and neurological abnormalities. It was first described by Dr. David Weaver in 1974. It is similar to Sotos syndrome.