Autism is a pervasive developmental disorder of unknown etiology. It is likely caused by mutations in one or more genes. One approach to understanding the molecular changes that occur in autism is to measure gene expression in post-mortem brain samples from individuals diagnosed with autism. This may be accomplished with techniques such as cDNA microarrays or subtractive hybridization. In general, gene expression is regulated as a function of body region, developmental time, and physiological state. A premise of the approaches we describe is that gene expression is regulated in cells from autistic individuals as a consequence of the disease process. It may be useful to detect such changes in order to identify selective biological markers for autism. Additionally, the abnormal regulation of gene expression may reveal cellular pathways that have been disrupted, suggesting strategies for therapeutic intervention.