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.

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.

The term "multisystem developmental disorder" has also been used to describe various developmental disorders. These include:

- Alagille syndrome, an autosomal dominant disorder with a wide range of features and manifestations. Its five most significant features are chronic cholestasis, a condition where bile cannot flow from the liver to the duodenum, occurring in 95% of cases; heart abnormalities (over 90%); butterfly vertebrae; posterior embryotoxon and a distinctive face (prominent forehead, deep-set eyes, and a pointed chin).

- Rubinstein-Taybi syndrome, a mental retardation syndrome characterized by broad thumbs, facial abnormalities, and big toes alongside mental retardation.

- Williams syndrome, a neurodevelopmental disorder characterized by a unique profile of strengths and deficits; most with the condition have mild mental retardation but have grammatical and lexical abilities above what would be expected from their IQs. They are hypersocial and empathetic, but social isolation is commonly experienced.

- Proteus syndrome, a congenital disorder causing disproportionate growth of skin, bone, and other tissues.

- Asphyxiating thoracic dysplasia, a autosomal recessive skeletal disorder with an estimated prevalence of between 1 in 100,000 and 1 in 130,000 live births.

Multisystem developmental disorder (MSDD) is a term used by Stanley Greenspan to describe children under age 3 who exhibit signs of impaired communication as in autism, but with strong emotional attachments atypical of autism. It is described in the DC:0-3R manual as an optional diagnosis for children under two years of age.

The scientific study of the causes of developmental disorders involves many different theories. Some of the major differences between these theories involves whether or not environment disrupts normal development, or if abnormalities are pre-determined.

Normal development occurs with a combination of contributions from both the environment and genetics. The theories vary in the part each factor has to play in normal development, thus affecting how the abnormalities are caused.

One theory that supports environmental causes of developmental disorders involves stress in early childhood. Researcher and child psychiatrist Bruce D. Perry, M.D., Ph.D, theorizes that developmental disorders can be caused by early childhood traumatization. In his works he compares developmental disorders in traumatized children to adults with post-traumatic stress disorder, linking extreme environmental stress to the cause of developmental difficulties. Other stress theories suggest that even small stresses can accumulate to result in emotional, behavioral, or social disorders in children.

A 2017 study tested all 20,000 genes in about 4,300 families with children with rare developmental difficulties in the UK and Ireland in order to identify if these difficulties had a genetic cause.They found 14 new developmental disorders caused by spontaneous genetic mutations not found in either parent (such as a fault in the CDK13 gene). They estimated that about one in 300 children are born with spontaneous genetic mutations associated with rare developmental disorders.

There are a number of factors that could potentially contribute to the development of feeding and eating disorders of infancy or early childhood. These factors include:

- Physiological – a chemical imbalance effecting the child's appetite could cause a feeding or eating disorder.

- Developmental – developmental abnormalities in oral-sensory, oral-motor, and swallowing can impact the child's eating ability and elicit a feeding or eating disorder.

- Environmental – simple issues such as inconsistent meal times can cause a feeding or eating disorder. Giving the child food that they are not developmentally acquired for can also cause these disorders. Family dysfunction and sociocultural issues could also play a role in feeding or eating disorders.

- Relational – when the child is not securely attached to the mother, it can cause feeding interactions to become disturbed or unnatural. Other factors, such as parental emotional unavailability and parental eating disorders, can cause feeding and eating disorders in their children.

- Psychological and behavioral – these factors include one involving the child's temperament. Characteristics such as being anxious, impulsive, distracted, or strong-willed personality types are ones that could affect the child's eating and cause a disorder. The individual could have learned to reject food due to a traumatic experience such as choking or being force fed.

While only a few adults have been reported with 2q37 microdeletion syndrome, it is predicted that this number will rise as various research studies continue to demonstrate that most with the disorder do not have a shortened life span.

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.

Developmental coordination disorder is a lifelong neurological condition that is more common in males than in females, with a ratio of approximately four males to every female. The exact proportion of people with the disorder is unknown since the disorder can be difficult to detect due to a lack of specific laboratory tests, thus making diagnosis of the condition one of elimination of all other possible causes/diseases. Approximately 5–6% of children are affected by this condition.

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.

There is no specific treatment for micro syndrome, but there are ways to help the disorders, and illnesses that come with it. Many individuals with Micro Syndrome need permanent assistance from their disorders and inabilities to move and support themselves. Seizures are not uncommon and patients should get therapy to help control them, and many patients also require wheelchairs to move, so an assistant would be needed at all times.

Those with micro syndrome are born appearing normal. At the age of one, mental and physical delays become apparent, along with some limb spasms. By the age of eight micro syndrome has already set in, and the patient will have joint contractures, Ocular Atrophy will become noticeable, the patient will most likely lose ability to walk, speak, and sometimes move at all.

The tenth revision of the International Statistical Classification of Diseases and Related Health Problems (ICD-10) has four categories of specific developmental disorder: specific developmental disorders of speech and language, specific developmental disorders of scholastic skills, specific developmental disorder of motor function, and mixed specific developmental disorder.

Autism spectrum disorders tend to be highly comorbid with other disorders. Comorbidity may increase with age and may worsen the course of youth with ASDs and make intervention/treatment more difficult. Distinguishing between ASDs and other diagnoses can be challenging, because the traits of ASDs often overlap with symptoms of other disorders, and the characteristics of ASDs make traditional diagnostic procedures difficult.

The most common medical condition occurring in individuals with autism spectrum disorders is seizure disorder or epilepsy, which occurs in 11-39% of individuals with ASD. Tuberous sclerosis, a medical condition in which non-malignant tumors grow in the brain and on other vital organs, occurs in 1-4% of individuals with ASDs.

Intellectual disabilities are some of the most common comorbid disorders with ASDs. Recent estimates suggest that 40-69% of individuals with ASD have some degree of an intellectual disability, more likely to be severe for females. A number of genetic syndromes causing intellectual disability may also be comorbid with ASD, including fragile X syndrome, Down syndrome, Prader-Willi and Angelman syndromes, and Williams syndrome.

Learning disabilities are also highly comorbid in individuals with an ASD. Approximately 25-75% of individuals with an ASD also have some degree of a learning disability.

Various anxiety disorders tend to co-occur with autism spectrum disorders, with overall comorbidity rates of 7-84%. Rates of comorbid depression in individuals with an ASD range from 4–58%. The relationship between ASD and schizophrenia remains a controversial subject under continued investigation, and recent meta-analyses have examined genetic, environmental, infectious, and immune risk factors that may be shared between the two conditions.

Deficits in ASD are often linked to behavior problems, such as difficulties following directions, being cooperative, and doing things on other people's terms. Symptoms similar to those of attention deficit hyperactivity disorder (ADHD) can be part of an ASD diagnosis.

Sensory processing disorder is also comorbid with ASD, with comorbidity rates of 42–88%.

Several prenatal and perinatal complications have been reported as possible risk factors for autism. These risk factors include maternal gestational diabetes, maternal and paternal age over 30, bleeding after first trimester, use of prescription medication (e.g. valproate) during pregnancy, and meconium in the amniotic fluid. While research is not conclusive on the relation of these factors to autism, each of these factors has been identified more frequently in autistic children compared to their non-autistic siblings and other normally developing youth.

Low vitamin D levels in early development has been hypothesized as a risk factor for autism.

Specific developmental disorders are disorders in which development is delayed in one specific area or areas, and in which basically all other areas of development are not affected. Specific developmental disorders are as opposed to pervasive developmental disorders that are characterized by delays in the development of multiple basic functions including socialization and communication.

Developmental disorders comprise a group of psychiatric conditions originating in childhood that involve serious impairment in different areas. There are several ways of using this term. The most narrow concept is used in the category "Specific Disorders of Psychological Development" in the ICD-10. These disorders comprise language disorders, learning disorders, motor disorders and autism spectrum disorders. In broader definitions ADHD is included, and the term used is neurodevelopmental disorders. Yet others include antisocial behavior and schizophrenia that begins in childhood and continues through life. However, these two latter conditions are not as stable as the other developmental disorders, and there is not the same evidence of a shared genetic liability.

Developmental disorders are present from early life. They usually improve as the child grows older, but they also entail impairments that continue through adult life. There is a strong genetic component, and more males are afflicted than females.

YVS has been described relatively recently in the 1980s and since then less than 15 cases have been reported around the world. Many of the infants did not survive beyond one year of age.

This is an ill-defined disorder of uncertain nosological validity. The category is included here because of the evidence that children with moderate to severe intellectual disability (IQ below 35) who exhibit major problems in hyperactivity and inattention frequently show stereotyped behaviours; such children tend not to benefit from stimulant drugs (unlike those with an IQ in the normal range) and may exhibit a severe dysphoric reaction (sometimes with psychomotor retardation) when given stimulants; in adolescence the overactivity tends to be replaced by underactivity (a pattern that is not usual in hyperkinetic children with normal intelligence). It is also common for the syndrome to be associated with a variety of developmental delays, either specific or global. The extent to which the behavioural pattern is a function of low IQ or of organic brain damage is not known, neither is it clear whether the disorders in children with mild intellectual disability who show the hyperkinetic syndrome would be better classified here or under F90.- (Hyperkinetic disorders); at present they are included in F90-.

Diagnostic guidelines

Diagnosis depends on the combination of developmentally inappropriate severe overactivity, motor stereotypies, and moderate to severe intellectual disability; all three must be present for the diagnosis. If the diagnostic criteria for F84.0 (childhood autism), F84.1 (atypical autism) or F84.2 (Rett's syndrome) are met, that condition should be diagnosed instead.

There have been 30 cases of Marden-Walker Syndrome reported since 1966. The first case of this was in 1966 a female infant was diagnosed with blepharophimosis, joint contractures, arachnodactyly and growth development delay. She ended up passing at 3 months due to pneumonia.

1p36 deletion syndrome (also known as monosomy 1p36) is a congenital genetic disorder characterized by moderate to severe intellectual disability, delayed growth, hypotonia, seizures, limited speech ability, malformations, hearing and vision impairment, and distinct facial features. The symptoms may vary, depending on the exact location of the chromosomal deletion.

The condition is caused by a genetic deletion (loss of a segment of DNA) on the outermost band on the short arm (p) of chromosome 1. It is one of the most common deletion syndromes. It is estimated that the syndrome occurs in one in every 5,000 to 10,000 births. Knowledge of the disorder has increased a great deal over the last decade, mainly because more patients have been accurately diagnosed and described in international medical literature.

The true prevalence of PMS has not been determined. More than 1200 people have been identified worldwide according the Phelan-McDermid Syndrome Foundation. However, it is believed to be underdiagnosed due to inadequate genetic testing and lack of specific clinical features. It is known to occur with equal frequency in males and females. Studies using chromosomal microarray for diagnosis indicate that at least 0.5% of cases of ASD can be explained by mutations or deletions in the "SHANK3" gene. In addition when ASD is associated with ID, "SHANK3" mutations or deletions have been found in up to 2% of individuals.

The collecting system is the structure that collects urine directly from the kidney tissue and routes it by way of the ureter to the bladder. Structural renal abnormalities are rare in both sexes.

Prognosis varies widely depending on severity of symptoms, degree of intellectual impairment, and associated complications. Because the syndrome is rare and so newly identified, there are no long term studies.

2q37 deletion syndrome is a disorder caused by the deletion of a small piece of chromosome 2.2q37 deletion syndrome describes a disorder in which one or multiple of 3 sub-bands, 2q37.1, 2q37.2, and 2q37.3, of the last band of one of the chromosome 2’s long arms are deleted. The first report of this disorder was in 1989.