Five family-based cohorts of European descent and a population-based case-control sample from Denmark were combined to discover five loci associated with autism spectrum disorder. In each family study, diagnosis was confirmed for all affected individuals using standard research tools and expert clinical consensus diagnosis. In the population-based cohort, cases were identified using the Danish Psychiatric Central Research Register and were diagnosed with ASD before 2013 by a psychiatrist according to ICD-10. All subjects in this sample were included here (18,381 cases; 27,969 controls).