Recent advances in high throughput genomic technologies, coupled with large patient cohorts and and an evolving culture of rapid data sharing have led to remarkable advances in the understanding of the genetics of autism spectrum disorders. To date, the lion’s share of this progress has been with regard to the contribution of rare and de novo mutations, both in DNA sequence and chromosomal structure. The ability now to reliably and systematically identify ASD risk genes and loci provides important initial insights into both the opportunities as well as the challenges the field now faces in moving from gene discovery to an actionable understanding of pathophysiological mechanisms underlying these complex common neurodevelopmental syndromes. The lecture will provide an overview of what is now known about the genomic architecture and specific risk mutations associated with ASD, address the particular challenges posed by the discovery of mutations that have large biological effect but low population allele frequency, and consider the role that whole genome sequencing will play in the near future in enhancing the understanding of the developmental aspects of ASD risk.