The human genome contains conserved loci that show accelerated divergence from other species — called human accelerated regions (HARs) — but the effect of mutations in these regions on brain function is poorly understood. Doan et al. found that the levels of two types of mutations — de novo copy-number variations and biallelic point mutations — were increased in HARs of people with autism spectrum disorder (ASD) compared with healthy individuals. Furthermore, they found that these mutations were located in the enhancer sequences of genes that were previously implicated in this disorder and brain function, suggesting a potential role for mutations in HARs in ASD and cognition.