Chromosomal abnormalities have been identified in some individuals with Autism Spectrum Disorder (ASD), but their full etiologic role is unknown. Submicroscopic copy number variation (CNV) represents a considerable source of genetic variation in the human genome that contributes to phenotypic differences and disease susceptibility. To explore the contribution CNV imbalances in ASD, we genotyped unrelated ASD index cases using the Affymetrix GeneChip® 500K single nucleotide polymorphism (SNP) mapping array. Keywords: Whole Genome Mapping SNP Genotyping Array Overall design: DNA derived from blood or lymphopblasts was hybridized to Affymetrix GeneChip® 500K mapping arrays. In total, 426 unrelated probands were analyzed along with 232 parents (116 trios). NspI and StyI arrays were analyzed for CNV using a combination of DNA Chip Analyzer (dChip), Copy Number Analysis for GeneChip (CNAG), and Genotyping Microarray based CNV Analysis (GEMCA).