Autism spectrum disorder is a heterogeneous, behaviorally defined, neurodevelopmental disorder that occurs in 1 in 150 children. Individuals with autism have deficits in social interaction and verbal and nonverbal communication and have restricted or stereotyped patterns of behavior. They might also have co-morbid disorders including intellectual impairment, seizures and anxiety. Postmortem and structural magnetic resonance imaging studies have highlighted the frontal lobes, amygdala and cerebellum as pathological in autism. However, there is no clear and consistent pathology that has emerged for autism. Moreover, recent studies emphasize that the time course of brain development rather than the final product is most disturbed in autism. We suggest that the heterogeneity of both the core and co-morbid features predicts a heterogeneous pattern of neuropathology in autism. Defined phenotypes in larger samples of children and well-characterized brain tissue will be necessary for clarification of the neuroanatomy of autism.