The neurobiology and neuropathology of the autism spectrum disorders (ASD) remain poorly defined. Brain imaging studies suggest that the deficits in social cognition, language, communication and stereotypical patterns of behaviour that are manifest in individuals with ASD, are related to functional disturbance and ‘disconnectivity’, affecting multiple brain regions. These impairments are considered to arise as a consequence of abnormal pre- and postnatal development of a distributed neural network. Examination of the brain post mortem continues to provide fundamental information concerning the cellular and subcellular alterations that take place in the brain of autistic individuals. Neuropathological observations that have emerged over the past decade also point towards early pre- and postnatal developmental abnormalities that involve multiple regions of the brain, including the cerebral cortex, cortical white matter, amygdala, brainstem and cerebellum. However, the neuropathology of autism is yet to be clearly defined, and there are several areas that remain open to further investigation. In this respect, more concerted efforts are required to examine the various aspects of cellular pathology affecting the brain in autism. This paper briefly highlights four key areas that warrant further evaluation.