Although many alternative therapies and interventions are available, few are supported by scientific studies. Treatment approaches have little empirical support in quality-of-life contexts, and many programs focus on success measures that lack predictive validity and real-world relevance. Scientific evidence appears to matter less to service providers than program marketing, training availability, and parent requests. Some alternative treatments may place the child at risk. A 2008 study found that compared to their peers, autistic boys have significantly thinner bones if on casein-free diets; in 2005, botched chelation therapy killed a five-year-old child with autism. There has been early research looking at hyperbaric treatments in children with autism.

Although popularly used as an alternative treatment for people with autism, there is no good evidence that a gluten-free diet is of benefit. In the subset of people who have gluten sensitivity there is limited evidence that suggests that a gluten free diet may improve some autistic behaviors.

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

No medications directly treat the core symptoms of AS. Although research into the efficacy of pharmaceutical intervention for AS is limited, it is essential to diagnose and treat comorbid conditions. Deficits in self-identifying emotions or in observing effects of one's behavior on others can make it difficult for individuals with AS to see why medication may be appropriate. Medication can be effective in combination with behavioral interventions and environmental accommodations in treating comorbid symptoms such as anxiety disorder, major depressive disorder, inattention and aggression. The atypical antipsychotic medications risperidone and olanzapine have been shown to reduce the associated symptoms of AS; risperidone can reduce repetitive and self-injurious behaviors, aggressive outbursts and impulsivity, and improve stereotypical patterns of behavior and social relatedness. The selective serotonin reuptake inhibitors (SSRIs) fluoxetine, fluvoxamine, and sertraline have been effective in treating restricted and repetitive interests and behaviors.

Care must be taken with medications, as side effects may be more common and harder to evaluate in individuals with AS, and tests of drugs' effectiveness against comorbid conditions routinely exclude individuals from the autism spectrum. Abnormalities in metabolism, cardiac conduction times, and an increased risk of type 2 diabetes have been raised as concerns with these medications, along with serious long-term neurological side effects. SSRIs can lead to manifestations of behavioral activation such as increased impulsivity, aggression, and sleep disturbance. Weight gain and fatigue are commonly reported side effects of risperidone, which may also lead to increased risk for extrapyramidal symptoms such as restlessness and dystonia and increased serum prolactin levels. Sedation and weight gain are more common with olanzapine, which has also been linked with diabetes. Sedative side-effects in school-age children have ramifications for classroom learning. Individuals with AS may be unable to identify and communicate their internal moods and emotions or to tolerate side effects that for most people would not be problematic.

There is no known cure for autism, although those with Asperger syndrome and those who have autism and require little-to-no support are more likely to experience a lessening of symptoms over time. The main goals of treatment are to lessen associated deficits and family distress, and to increase quality of life and functional independence. In general, higher IQs are correlated with greater responsiveness to treatment and improved treatment outcomes. Although evidence-based interventions for autistic children vary in their methods, many adopt a psychoeducational approach to enhancing cognitive, communication, and social skills while minimizing problem behaviors. It has been argued that no single treatment is best and treatment is typically tailored to the child's needs.

Intensive, sustained special education programs and behavior therapy early in life can help children acquire self-care, social, and job skills. Available approaches include applied behavior analysis, developmental models, structured teaching, speech and language therapy, social skills therapy, and occupational therapy. Among these approaches, interventions either treat autistic features comprehensively, or focus treatment on a specific area of deficit. Generally, when educating those with autism, specific tactics may be used to effectively relay information to these individuals. Using as much social interaction as possible is key in targeting the inhibition autistic individuals experience concerning person-to-person contact. Additionally, research has shown that employing semantic groupings, which involves assigning words to typical conceptual categories, can be benevficial in fostering learning.

There has been increasing attention to the development of evidence-based interventions for young children with ASD. Two theoretical frameworks outlined for early childhood intervention include applied behavioral analysis (ABA) and the developmental social-pragmatic model (DSP). Although ABA therapy has a strong evidence base, particularly in regard to early intensive home-based therapy. ABA's effectiveness may be limited by diagnostic severity and IQ of the person affected by ASD. The Journal of Clinical Child and Adolescent Psychology has deemed two early childhood interventions as “well-established”: individual comprehensive ABA, and focused teacher-implemented ABA combined with DSP.

Another evidence-based intervention that has demonstrated efficacy is a parent training model, which teaches parents how to implement various ABA and DSP techniques themselves. Various DSP programs have been developed to explicitly deliver intervention systems through at-home parent implementation.

A multitude of unresearched alternative therapies have also been implemented. Many have resulted in harm to autistic people and should not be employed unless proven to be safe.

In October 2015, the American Academy of Pediatrics (AAP) proposed new evidence-based recommendations for early interventions in ASD for children under 3. These recommendations emphasize early involvement with both developmental and behavioral methods, support by and for parents and caregivers, and a focus on both the core and associated symptoms of ASD.

Asperger syndrome treatment attempts to manage distressing symptoms and to teach age-appropriate social, communication and vocational skills that are not naturally acquired during development, with intervention tailored to the needs of the individual based on multidisciplinary assessment. Although progress has been made, data supporting the efficacy of particular interventions are limited.

Neurodevelopmental disorders are in their multitude associated with widely varying degrees of difficulty, depending on which there are different degrees of mental, emotional, physical, and economic consequences for individuals, and in turn families, groups and society.

Loss of language and skills related to social interaction and self-care are serious. The affected children face ongoing disabilities in certain areas and require long term care. Treatment of CDD involves both behavior therapy, environmental therapy and medications.

- Behavior therapy: The main aim of Applied Behavior Analysis (ABA) is to systematically teach the child to relearn language, self-care and social skills. The treatment programs designed in this respect "use a system of rewards to reinforce desirable behaviors and discourage problem behavior." ABA programs may be designed by a board-certified specialist in behavior analysis called a "BCBA" (Board Certified Behavior Analyst), but ABA is also widely used by a number of other health care personnel from different fields like psychologists, speech therapists, physical therapists and occupational therapists with differing levels of expertise. Parents, teachers and caregivers are instructed to use these behavior therapy methods at all times.

- Environmental Therapy: Sensory Enrichment Therapy uses enrichment of the sensory experience to improve symptoms in autism, many of which are common to CDD.

- Medications: There are no medications available to directly treat CDD. Antipsychotic medications are used to treat severe behavior problems like aggressive stance and repetitive behavior patterns. Anticonvulsant medications are used to control seizures.

Medications are used to address certain behavioral problems; therapy for children with PDD should be specialized according to the child's specific needs.

Some children with PDD benefit from specialized classrooms in which the class size is small and instruction is given on a one-to-one basis. Others function well in standard special education classes or regular classes with support. Early intervention, including appropriate and specialized educational programs and support services, play a critical role in improving the outcome of individuals with PDD.

There is currently no specific treatment for megalencephaly, however periodic head measurements may be assessed to determine the rate of brain growth.

Those individuals who develop neurological disorders may be prescribed anti-epileptic drugs for seizures. Studies have shown that reducing epilepsy can increase cell apoptosis and reduce the proliferation of neurons that ultimately leads to brain overgrowth.

Brain trauma in the developing human is a common cause (over 400,000 injuries per year in the US alone, without clear information as to how many produce developmental sequellae) of neurodevelopmental syndromes. It may be subdivided into two major categories, congenital injury (including injury resulting from otherwise uncomplicated premature birth) and injury occurring in infancy or childhood. Common causes of congenital injury are asphyxia (obstruction of the trachea), hypoxia (lack of oxygen to the brain) and the mechanical trauma of the birth process itself.

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.

Since there are very few treatment methods focused on managing megalencephaly, future research is targeted at inhibiting mutation of the pathway. However, this next step could be met with several complications as understanding the underlying mechanism of the mutation is a difficult task. The genetic coding that initiates a single mutation is sporadic and patterns are hard to detect in many cases.

Even thought very little research has been done to create inhibitors of the PI3K-AKT pathway, several pharmaceutical companies have begun to focus their interests in designing a prevention method for this purpose.

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.

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.

There is no known "cure" for PDD-NOS, but there are interventions that can have a positive influence. Early and intensive implementation of evidence-based practices and interventions are generally believed to improve outcomes. Most of these are individualized special education strategies rather than medical or pharmaceutical treatment; the best outcomes are achieved when a team approach among supporting individuals is utilized.

Some of the more common therapies and services include:

- Visual and environmental supports, visual schedules

- Applied behavior analysis

- Discrete trial instruction (part of applied behavior analysis)

- Social stories and comic strip conversations

- Physical and occupational therapy

Fragile X syndrome is the most translated neurodevelopmental disorder under study. The increased understanding of the molecular mechanisms of disease in FXS has led to the development of therapies targeting the affected pathways. Evidence from mouse models shows that mGluR5 antagonists (blockers) can rescue dendritic spine abnormalities and seizures, as well as cognitive and behavioral problems, and may show promise in the treatment of FXS. Two new drugs, AFQ-056 (mavoglurant) and dipraglurant, as well as the repurposed drug fenobam are currently undergoing human trials for the treatment of FXS. There is also early evidence for the efficacy of arbaclofen, a GABA agonist, in improving social withdrawal in individuals with FXS and ASD.

In addition, there is evidence from mouse models that minocycline, an antibiotic used for the treatment of acne, rescues abnormalities of the dendrites. An open trial in humans has shown promising results, although there is currently no evidence from controlled trials to support its use.

The first complete DNA sequence of the repeat expansion in someone with the full mutation was generated by scientists in 2012 using SMRT sequencing.

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.

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.

Treatments for HFA address individual symptoms, rather than the condition as a whole. For instance, to treat anxiety, which is often associated with HFA, the main treatment is cognitive behavior therapy. While this is the tested and approved treatment for anxiety, it does not quite meet the needs associated with the symptoms of HFA. There is very little discussion of the parent's role in anxiety intervention for children and teenagers. A revised version of cognitive behavior therapy has parents and teachers acting in a role as social coaches to help the children or young adults cope with the issues they are facing. There have been several trials proving that the involvement of parents in the lives of the children affected with anxiety associated with HFA is important.

No single intervention exists to aid individuals with high-functioning autism. However, there are proactive strategies, such as self care and self-management, designed to maintain or change behavior to make living with high functioning autism easier. Self-management strategies aim to provide skills necessary to self-regulate behavior, leading to greater levels of independence. Improving self-management skills allows the individual to be more self-reliant rather than having to rely on an external source for supervision or control. Self-monitoring is a framework, not a rigid structure, designed to encourage independence and self-control. Self-monitoring is not for everyone. It requires the attention and dedication of the individual with high-functioning autism as well as the individual overseeing the progress.

A framework for self-monitoring is provided below

- Identify positive target behaviors

- Establish an alternative behavior that is positive/constructive

- Establish a self-recording sheet

- Individuals can make sure to stay on track with intended goals

- Set goals and keep them

The goal of self-monitoring is to enforce self-monitoring independently without prompting.

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.

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.

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.

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 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.

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.