Reports of unrelated individuals with autism spectrum disorder (ASD) and similar clinical features having overlapping de novo interstitial deletions at 2p15–p16. 1 suggest that this region harbors a gene (s) important to the development of autism. We molecularly characterized two such deletions, selecting two genes in this region, exportin 1 (XPO1) and orthodenticle homolog 1 (OTX1) for association studies in three North American cohorts (Autism Spectrum Disorder–Canadian American Research Consortium (ASD–CARC), New York, and Autism Genetic Resource Exchange (AGRE)) and one Italian cohort (Società Italiana per la Ricerca e la Formazione sull’Autismo (SIRFA)) of families with ASD. In XPO1, rs6735330 was associated with autism in all four cohorts (P< 0.05), being significant in ASD–CARC cohorts (P-value following false discovery rate correction for multiple testing (P FDR)= 1.29× 10− 5), the AGRE cohort (P FDR= 0.0011) and the combined families (P FDR= 2.34× 10− 9). Similarly, in OTX1, rs2018650 and rs13000344 were associated with autism in ASD–CARC cohorts (P FDR= 8.65× 10− 7 and 6.07× 10 5, respectively), AGRE cohort (P FDR= 0.0034 and 0.015, respectively) and the combined families (P FDR= 2.34× 10− 9 and 0.00017, respectively); associations were marginal or insignificant in the New York and SIRFA cohorts. A significant association (P FDR= 2.63× 10− 11) was found for the rs2018650G–rs13000344C haplotype. The above three SNPs were associated with severity of social interaction and verbal communication deficits and repetitive behaviors (P-values< 0.01). No additional deletions were identified following screening of 798 ASD individuals. Our results indicate that deletion 2p15–p16. 1 is not commonly associated with idiopathic ASD, but represents a novel contiguous gene syndrome associated with a constellation of phenotypic features (autism, intellectual disability, craniofacial/CNS dysmorphology), and that XPO1 and OXT1 may contribute to ASD in 2p15–p16. 1 deletion cases and non-deletion cases of ASD mapping to this chromosome region.