For all the research into the causes of autism, doctors have concluded that autism is an abnormality of the brain and/or the way that the brain functions and how it interprets information. However, the exact mechanism of that abnormality continues to allude them. It is unknown whether autism is a series of interacting abnormalities in the brain or whether it is one single abnormality. What they do know is that whether autism consists of several abnormalities or one abnormality, it changes the way that the entire brain works. These studies also confirm that the abnormality causes neural differences as early as soon after conception. It is thought that the abnormality begins to affect the brain as it develops in the womb, affected during the course of its progression by environmental factors. There is definitely a difference between an autistic brain and a neurotypal brain - autopsies of deceased autistic children have shown that their brain, skull size, and head circumference are larger than typical.

A few opinions on the mechanism behind autism have come from the few observations. One possibility is that the initial abnormality is too many neurons that can cause overconnectivity, thus overstimulation, in some important areas in the brain. Another possibility is that neuron paths are interrupted during gestation, which requires a redirecting of neural paths that are atypical. Yet another possibility are abnormally constructed neural dendrites and synapses, which would impact how stimuli was processed - this kind of abnormality also contributes to epilepsy, which is often associated with autism.

Then there is the researched correlation between immune sensitivity and autism. Immune development and neurodevelopment happen around the same time, and the immune system and nervous system tend to interact very much at that place in general development. So it is possible that an abnormal immune development can contribute to a poor neurodevelopment, or vice versa. However, the connection is not absolute (for instance, that kind of immune sensitivity is absent in many autism cases and present in many people without autism) and remains a controversial one. There is another theory that the mirror neural system (which is a neural system responsible for imitation) is impaired during development, which is why autistic people have such a hard time doing things as others do them and have difficulty in social situations and responding to social and verbal cues.

In general, the present consensus between researchers is that autism causes trouble or less activity within high-level neural processes while low-level neural processes show overactivity. This tends to show up in brain function studies that show differences between how the autistic person interprets information during social and non-social situations. Pathways of brain processing are different in the autistic individual in comparison to the neurotypal individual. The frontal lobe and parts of the cortex that control these high-level neural processes tend to show not enough activity during these studies, while other parts of the cortex in charge of low-level neural processes show much more than usual activity. This means that high-level neural processes like empathy, imitation, memory and other skills important in human social interaction are impaired and can lead to a reversion into withdrawing, repetitive movements and language, or extreme or inappropriate emotional response.