Autism is a neurodevelopmental disorder characterized by impairments in social interactions, communication, and behavior. Multiple lines of evidence support the notion that most cases of autism likely have an underlying genetic cause or predisposition. Like mental retardation, autism is likely to be caused by many different genetic mechanisms and genes rather than a single, or few, major genes or environmental effects. In this review, we will focus on the cytogenetic contribution to uncovering regions of the genome involved in autism. Some common cytogenetic imbalances already known to cause autism will be highlighted. Routine genetic testing in clinical (CLIA-certified) diagnostic laboratories can identify the specific etiology and recurrence risk in 10% to 15% of autism cases and is clinically indicated for any child with autism. Powerful new methods for identifying novel regions of the genome causing or contributing to autism also will be discussed and will start to explain the etiology for some percentage of the remaining 85% to 90% of autism cases.