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First, people with Asperger's Syndrome usually view themselves as having a brain that functions differently, not one that is damaged. There are differences in the brain, but that does not mean it is brain damage. It could be simply a brain that develops atypically.

Some studies indicate that people with autism or Asperger's Syndrome have brains that are different, but not damaged, although some individuals could have brain damage, as well. Some studies indicate there is damage. So, it is possible that brain damage causes Asperger's Syndrome in some cases but not in others. In addition, since people with autism and Asperger's Syndrome are more likely than average to have certain comorbid conditions, such as mental retardation and epilepsy, it can be more difficult to determine whether brain differences are attributable to the autism spectrum disorder or one of the comorbid conditions.

Van Krevelen suggested that autism results from the combination of autism genes and brain damage, while Asperger's Syndrome comes from the autism genes without brain damage. At least one study provides some support for this theory, but it could be a matter of the severity and extent of the brain damage. So, more research would need to be done to confirm this theory.

There are studies indicating that Asperger's Syndrome is a right hemisphere disorder. (A discussion of this theory and mention of various studies can be found in the book Asperger Syndrome: A Gift or a Curse? by Viktoria Lyons amd Michael Fitzgerald.) They discuss the functions of the right hemisphere and left hemisphere, describing how behaviors could be similar to autism and Asperger's Syndrome if there were a right hemisphere impairment.

Several studies have shown that the amygdala is different. Brain imaging studies show that the amygdala reaches adult-size in boys with autism years before it happens in boys who do not have autism. Amaral and Schumann found a lower number of neurons in the amygdala in males with autism.

Some studies have shown differences in the frontal lobe cortex, the hippocampus, the cerebellum, the brain stem, etc. There are multiple differences.

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