How does autism affect the brain?

It's complicated... Autism spectrum disorder (ASD) is a range of complex neurodevelopment disorders characterized by persistent impairments in social communication, and restrictive, repetitive, and stereotyped patterns of behaviors, interests, or activities. How it affects the brain itself is more complicated. Go to NINDS.NIH.GOV and search: Autism, for more detailed answers. Consult a HealthTap provider as needed.
Intense research. Autism spectrum disorder is being studied by some of the best laboratories in the world. Molecularly there have been alternations noted in epigenetic areas, and positron emission tomography has revealed alterations in virtually all neurotransmitters. It thus is extraordinarily complex.
Different ways. Typically those with autism have impaired social skills, sometimes poor eye contact, perhaps lanugage or learning problems, stereotypical behavior, repetitive behavior, sometimes sensativities to textures, sounds, tastes, smells, or changes in routine. Autism is a spectrum disorder and some have it severe, some have it very mild, each person is different. Many children also suffer from GI prob.
Many different way. Autism causes mild to significant changes to a diverse number brain processing centers.