While infection with rubella during pregnancy causes fewer than 1% of cases of autism, vaccination against rubella can prevent many of those cases.

There is no known cure. Children recover occasionally, so that they lose their diagnosis of ASD; this occurs sometimes after intensive treatment and sometimes not. It is not known how often recovery happens; reported rates in unselected samples of children with ASD have ranged from 3% to 25%. Most children with autism acquire language by age five or younger, though a few have developed communication skills in later years. Most children with autism lack social support, meaningful relationships, future employment opportunities or self-determination. Although core difficulties tend to persist, symptoms often become less severe with age.

Few high-quality studies address long-term prognosis. Some adults show modest improvement in communication skills, but a few decline; no study has focused on autism after midlife. Acquiring language before age six, having an IQ above 50, and having a marketable skill all predict better outcomes; independent living is unlikely with severe autism. Most people with autism face significant obstacles in transitioning to adulthood.

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.

The results of family and twin studies suggest that genetic factors play a role in the etiology of autism and other pervasive developmental disorders. Studies have consistently found that the prevalence of autism in siblings of autistic children is approximately 15 to 30 times greater than the rate in the general population. In addition, research suggests that there is a much higher concordance rate among monozygotic twins compared to dizygotic twins. It appears that there is no single gene that can account for autism. Instead, there seem to be multiple genes involved, each of which is a risk factor for components of the autism spectrum disorders.

There is some evidence that children with AS may see a lessening of symptoms; up to 20% of children may no longer meet the diagnostic criteria as adults, although social and communication difficulties may persist. As of 2006, no studies addressing the long-term outcome of individuals with Asperger syndrome are available and there are no systematic long-term follow-up studies of children with AS. Individuals with AS appear to have normal life expectancy, but have an increased prevalence of comorbid psychiatric conditions, such as major depressive disorder and anxiety disorder that may significantly affect prognosis. Although social impairment may be lifelong, the outcome is generally more positive than with individuals with lower functioning autism spectrum disorders; for example, ASD symptoms are more likely to diminish with time in children with AS or HFA. Most students with AS/HFA have average mathematical ability and test slightly worse in mathematics than in general intelligence, but some are gifted in mathematics. AS has potentially been linked to some accomplishments, such as Vernon L. Smith winning the Nobel Memorial Prize in Economic Sciences; however, Smith is self-diagnosed.

Although many attend regular education classes, some children with AS may utilize special education services because of their social and behavioral difficulties. Adolescents with AS may exhibit ongoing difficulty with self care or organization, and disturbances in social and romantic relationships. Despite high cognitive potential, most young adults with AS remain at home, yet some do marry and work independently. The "different-ness" adolescents experience can be traumatic. Anxiety may stem from preoccupation over possible violations of routines and rituals, from being placed in a situation without a clear schedule or expectations, or from concern with failing in social encounters; the resulting stress may manifest as inattention, withdrawal, reliance on obsessions, hyperactivity, or aggressive or oppositional behavior. Depression is often the result of chronic frustration from repeated failure to engage others socially, and mood disorders requiring treatment may develop. Clinical experience suggests the rate of suicide may be higher among those with AS, but this has not been confirmed by systematic empirical studies.

Education of families is critical in developing strategies for understanding strengths and weaknesses; helping the family to cope improves outcomes in children. Prognosis may be improved by diagnosis at a younger age that allows for early interventions, while interventions in adulthood are valuable but less beneficial. There are legal implications for individuals with AS as they run the risk of exploitation by others and may be unable to comprehend the societal implications of their actions.

Frequency estimates vary enormously. In 2015 it was estimated that 37.2 million people globally are affected. A 2003 review of epidemiological studies of children found autism rates ranging from 0.03 to 4.84 per 1,000, with the ratio of autism to Asperger syndrome ranging from 1.5:1 to 16:1; combining the geometric mean ratio of 5:1 with a conservative prevalence estimate for autism of 1.3 per 1,000 suggests indirectly that the prevalence of AS might be around 0.26 per 1,000. Part of the variance in estimates arises from differences in diagnostic criteria. For example, a relatively small 2007 study of 5,484 eight-year-old children in Finland found 2.9 children per 1,000 met the ICD-10 criteria for an AS diagnosis, 2.7 per 1,000 for Gillberg and Gillberg criteria, 2.5 for DSM-IV, 1.6 for Szatmari "et al.", and 4.3 per 1,000 for the union of the four criteria. Boys seem to be more likely to have AS than girls; estimates of the sex ratio range from 1.6:1 to 4:1, using the Gillberg and Gillberg criteria. Females with autism spectrum disorders may be underdiagnosed.

Anxiety disorder and major depressive disorder are the most common conditions seen at the same time; comorbidity of these in persons with AS is estimated at 65%. Reports have associated AS with medical conditions such as aminoaciduria and ligamentous laxity, but these have been case reports or small studies and no factors have been associated with AS across studies. One study of males with AS found an increased rate of epilepsy and a high rate (51%) of nonverbal learning disorder. AS is associated with tics, Tourette syndrome, and bipolar disorder, and the repetitive behaviors of AS have many similarities with the symptoms of obsessive–compulsive disorder and obsessive–compulsive personality disorder. However many of these studies are based on clinical samples or lack standardized measures; nonetheless, comorbid conditions are relatively common.

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.

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.

There are some who believe that regressive autism is simply early-onset autism that was recognized at a later date. Researchers have conducted studies to determine whether regressive autism is a distinct subset of autism spectrum disorders. Over the years, the results of these studies have contradicted one another. Some researchers believe there is still nothing to support a definitive biological difference between early-onset and regressive autism. However, emerging research shows that males with regressive autism have brains that are six percent larger than anyone with early-onset autism. The brains of females with regressive autism show no difference in brain size.

Regression in autism spectrum disorders is well documented; attribution of regression to environmental stress factors may result in a delay in diagnosis. The apparent onset of regressive autism is surprising and distressing to parents, who often initially suspect severe hearing loss. A controversy occurred following a fraudulent study linking MMR vaccine to autism, but since then, studies have shown no connection between autism and the MMR vaccine. There are also studies being done to test if certain types of regressive autism have an autoimmune basis.

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.

No widely accepted cognitive theory explains savants' combination of talent and deficit. It has been suggested that individuals with autism are biased towards detail-focused processing and that this cognitive style predisposes individuals either with or without autism to savant talents. Another hypothesis is that savants hyper-systemize, thereby giving an impression of talent. Hyper-systemizing is an extreme state in the empathizing–systemizing theory that classifies people based on their skills in empathizing with others versus systemizing facts about the external world. Also, the attention to detail of savants is a consequence of enhanced perception or sensory hypersensitivity in these unique individuals. It has also been confirmed that some savants operate by directly accessing low-level, less-processed information that exists in all human brains that is not normally available to conscious awareness.

Mind-blindness is a cognitive disorder where an individual is unable to attribute mental states to others. As a result of this kind of social and empathetic cognitive deficit, the individual is incapable in putting himself "into someone else's shoes" and cannot conceptualize, understand or predict knowledge, thoughts and beliefs, emotions, feelings and desires, behaviour, actions and intentions of another person. Such an ability to develop a mental awareness of what is in the other minds is known as the theory of mind (ToM), and the "Mind-blindness" Theory asserts that children who delay in this development often are or will be autistic and Asperger's syndrome (AS) patients. In addition to autism and AS, ToM and mind-blindness research has recently been extended to other disorders such as schizophrenia, dementia, bipolar disorders, antisocial personality disorders as well as normal aging.

All of the causes of childhood disintegrative disorder are still unknown. Sometimes CDD surfaces abruptly within days or weeks, while in other cases it develops over a longer period of time. A Mayo Clinic report indicates: "Comprehensive medical and neurological examinations in children diagnosed with childhood disintegrative disorder seldom uncover an underlying medical or neurological cause. Although the occurrence of epilepsy is higher in children with childhood disintegrative disorder, experts don't know whether epilepsy plays a role in causing the disorder."

CDD, especially in cases of later age of onset, has also been associated with certain other conditions, particularly the following:

- Lipid storage diseases: In this condition, a toxic buildup of excess fats (lipids) takes place in the brain and nervous system.

- Subacute sclerosing panencephalitis: Chronic infection of the brain by a form of the measles virus causes subacute sclerosing panencephalitis. This condition leads to brain inflammation and the death of nerve cells.

- Tuberous sclerosis (TSC): TSC is a genetic disorder. In this disorder, tumors may grow in the brain and other vital organs like kidneys, heart, eyes, lungs, and skin. In this condition, noncancerous (benign) tumors, hamartomas, grow in the brain.

- Leukodystrophy: In this condition, the myelin sheath does not develop in a normal way causing white matter in the brain to disintegrate.

A pervasive developmental disorder not otherwise specified (PDD-NOS) is one of the four autism spectrum disorders (ASD) and also one of the five disorders classified as a pervasive developmental disorder (PDD). According to the DSM-IV, PDD-NOS is a diagnosis that is used for "severe and pervasive impairment in the development of reciprocal social interaction or verbal and nonverbal communication skills, or when stereotyped behavior, interests, and activities are present, but the criteria are not met for a specific PDD" or for several other disorders. PDD-NOS is often called atypical autism, because the criteria for autistic disorder are not met, for instance because of late age of onset, atypical symptomatology, or subthreshold symptomatology, or all of these. Even though PDD-NOS is considered milder than typical autism, this is not always true. While some characteristics may be milder, others may be more severe.

It is common for individuals with PDD-NOS to have more intact social skills and a lower level of intellectual deficit than individuals with other PDDs. Characteristics of many individuals with PDD-NOS are:

- Communication difficulties (e.g., using and understanding language)

- Difficulty with social behavior

- Difficulty with changes in routines or environments

- Uneven skill development (strengths in some areas and delays in others)

- Unusual play with toys and other objects

- Repetitive body movements or behavior patterns

- Preoccupation with fantasy, such as imaginary friends in childhood

Mind-blindness is a state where the ToM has not been developed or lost in an individual. The ToM is implicit in neurotypical individuals. This enables one to make automatic interpretations of events taking into consideration the mental states of people, their desires and beliefs. Simon Baron-Cohen described an individual lacking a ToM would perceive the world in a confusing and frightening manner; leading to a withdrawal from society.

An alternative approach to the social impairment observed in mind-blindness focuses on emotion of subjects. Based on empirical evidence, Uta Frith concluded that the processing of complex cognitive emotions is impaired compared to simpler emotions. In addition, attachment does not seem to fail in the early childhood of autistics. This suggests that emotion is a component of social cognition that is separable from mentalizing.

Lombardo and Cohen updated the theory and pinpointed some additional factors that play an important part in ToM of autistic patients. They highlighted that the middle cingulated cortex which is outside the traditional mentalizing region was underactive in autistic patients, while the rest of ToM activation was normal. This region was important in deciding how much to invest in a person and hence required mentalization.

It is estimated that 25 to 50% of children diagnosed with Autism Spectrum Disorder (ASD) never develop spoken language beyond a few words or utterances. Despite the growing field of research on ASD, there is not much information available pertaining to individuals with autism who never develop functional language; that, in fact, individuals with nonverbal autism are considered to be underrepresented in all of autism research. Because of the limited research on nonverbal autism, there are not many validated measurements appropriate for this population. For example, while they may be appropriate for younger children, they lack the validity for grade-school aged children and adolescents and have continued to be a roadblock for nonverbal autism research. Often in autism research, individuals with nonverbal autism are sub-grouped with LFA, categorized by learning at most one word or having minimal verbal language.

Most of the existing body of research in nonverbal autism focuses on early interventions that predict successful language outcomes. Research suggests that most spoken language is inherited before the age of five, and the likelihood of acquiring functional language in the future past this age is minimal, that early language development is crucial to educational achievement, employment, independence during adulthood, and social relationships.

Males with pathogenic "MECP2" mutations usually die within the first 2 years from severe encephalopathy, unless they have an extra X chromosome (often described as Klinefelter syndrome), or have somatic mosaicism.

Male fetuses with the disorder rarely survive to term. Because the disease-causing gene is located on the X chromosome, a female born with an MECP2 mutation on her X chromosome has another X chromosome with an ostensibly normal copy of the same gene, while a male with the mutation on his X chromosome has no other X chromosome, only a Y chromosome; thus, he has no normal gene. Without a normal gene to provide normal proteins in addition to the abnormal proteins caused by a MECP2 mutation, the XY karyotype male fetus is unable to slow the development of the disease, hence the failure of many male fetuses with a MECP2 mutation to survive to term.

Females with a MECP2 mutation, however, have a non-mutant chromosome that provides them enough normal protein to survive longer. Research shows that males with Rett syndrome may result from Klinefelter's syndrome, in which the male has an XXY karyotype. Thus, a non-mutant "MECP2" gene is necessary for a Rett's-affected embryo to survive in most cases, and the embryo, male or female, must have another X chromosome.

There have, however, been several cases of 46,XY karyotype males with a MECP2 mutation (associated with classical Rett syndrome in females) carried to term, who were affected by neonatal encephalopathy and died before 2 years of age. The incidence of Rett syndrome in males is unknown, partly owing to the low survival of male fetuses with the Rett syndrome-associated MECP2 mutations, and partly to differences between signs caused by MECP2 mutations and those caused by Rett's.

Females can live up to 40 years or more. Laboratory studies on Rett syndrome may show abnormalities such as:

- EEG abnormalities from 2 years of age

- atypical brain glycolipids

- elevated CSF levels of "beta"-endorphin and glutamate

- reduction of substance P

- decreased levels of CSF nerve growth factors

A high proportion of deaths are abrupt, but most have no identifiable cause; in some instances death is the result most likely of:

- spontaneous brainstem dysfunction

- cardiac arrest, likely due to long QT syndrome, ventricular tachycardia or other arrhythmias

- seizures

- gastric perforation

A 2013 review stated that life expectancy for FXS was 12 years lower than the general population and that the causes of death were similar to those found for the general population.

Although not necessary for the diagnosis, individuals with intellectual disability are at higher risk for SMD. It is more common in boys, and can occur at any age.

Late talker is a term used for exceptionally bright people who experience a delay in the development of speech. Commonalities include usually being boys, delayed speech development, highly educated parents, musically gifted families, puzzle-solving abilities, and lagging social development. Many high-achieving late talkers were notoriously strong willed and noncompliant as children. Late talkers can often be misdiagnosed early on as having severe ("low-functioning") autism spectrum disorder (a category known simply as "autism", prior to the DSM-5), and careful professional evaluation is necessary for differential diagnosis, according to Darold Treffert and other experts. One major difference between late talkers and low-functioning autistic children is that for late talkers, communication skills automatically reach a normal level and the child requires no further special treatment with regards to speech. Outlook for late talkers with or without intervention is generally favorable. However, late language emergence can also be an early or secondary sign of high-functioning autism spectrum disorder / Asperger syndrome, or other developmental disorders, such as attention deficit hyperactivity disorder, intellectual disability, learning disability, social communication disorder, or specific language impairment.

Einstein syndrome, a term coined by the economist Thomas Sowell, is also sometimes used to describe late talkers. The term is named after Albert Einstein (often said to have been a late talker, though with questionable evidence), whom Sowell used as the primary example of a late talker in his work. Sowell also included Edward Teller, Srinivasa Ramanujan, the mathematician Julia Robinson, Richard Feynman, and the pianists Clara Schumann and Arthur Rubinstein to be in the late talkers group. As a toddler, the scientist John Clive Ward showed similar behavioral traits to those described by Sowell, according to a brief sketch of his biography.

Sowell claimed late talkers are often inaccurately categorized as having an autism spectrum disorder (ASD), and that a small subset of late talkers are highly intelligent children with common characteristics concentrated in music, memory, math or the sciences. However, as reported by Simon Baron-Cohen, such characteristics are often found in high-functioning autism / Asperger syndrome.

CDD is a rare condition, with only 1.7 cases per 100,000.

A child affected with childhood disintegrative disorder shows normal development and he/she acquires "normal development of age-appropriate verbal and nonverbal communication, social relationships, motor, play and self-care skills" comparable to other children of the same age. However, between the ages of 2 and 10, skills acquired are lost almost completely in at least two of the following six functional areas:

- Expressive language skills (being able to produce speech and communicate a message)

- Receptive language skills (comprehension of language - listening and understanding what is communicated)

- Social skills and self care skills

- Control over bowel and bladder

- Play skills

- Motor skills

Lack of normal function or impairment also occurs in at least two of the following three areas:

- Social interaction

- Communication

- Repetitive behavior and interest patterns

In her book, "Thinking in Pictures", Temple Grandin argues that compared to "Kanner's classic autism" and to Asperger syndrome, CDD is characterized with more severe sensory processing disorder but less severe cognitive problems. She also argues that compared to most autistic people, persons with CDD have more severe speech pathology and they usually do not respond well to stimulants.

The causes of nonverbal autism are unknown. However, there appears to be a relationship between joint attention and verbal communication. Joint attention occurs between two individuals when one draws the other’s attention to an object through gesturing (i.e. eye-gazing, pointing). The ability to achieve joint attention at an early age plays a significant role in language development, and studies indicate severe lapses in joint attention in children with autism. In one study, researchers suggest that a displayed pattern of delays, absences, or a general impaired response to stimuli (hyporesponsiveness) and a fascination with intense or repetitive stimulation (sensory seeking) is more likely in nonverbal children with autism, suggesting that both hyporesponsiveness and sensory seeking is related to poor communication outcomes in children with ASD.

Fragile X syndrome is a genetic disorder which occurs as a result of a mutation of the "fragile X mental retardation 1" ("FMR1") gene on the X chromosome, most commonly an increase in the number of CGG trinucleotide repeats in the 5' untranslated region of "FMR1". Mutation at that site is found in 1 out of about every 2000 males and 1 out of about every 259 females. Incidence of the disorder itself is about 1 in every 3600 males and 1 in 4000–6000 females. Although this accounts for over 98% of cases, FXS can also occur as a result of point mutations affecting "FMR1".

In unaffected individuals, the "FMR1" gene contains 5–44 repeats of the sequence CGG, most commonly 29 or 30 repeats. Between 45-54 repeats is considered a "grey zone", with a premutation allele generally considered to be between 55 and 200 repeats in length. Individuals with fragile X syndrome have a full mutation of the "FMR1" allele, with over 200 CGG repeats. In these individuals with a repeat expansion greater than 200, there is methylation of the CGG repeat expansion and "FMR1" promoter, leading to the silencing of the "FMR1" gene and a lack of its product.

This methylation of "FMR1" in chromosome band Xq27.3 is believed to result in constriction of the X chromosome which appears 'fragile' under the microscope at that point, a phenomenon that gave the syndrome its name. One study found that FMR1 silencing is mediated by the FMR1 mRNA. The FMR1 mRNA contains the transcribed CGG-repeat tract as part of the 5' untranslated region, which hybridizes to the complementary CGG-repeat portion of the FMR1 gene to form an RNA·DNA duplex.