Based on the substantial male bias in autism prevalence and the fact that two of the suspected neuroligin pathway genes are on the X-chromosome, we performed comprehensive sequencing of the NLGN3 (Xp13.1) and NLGN4X (Xp22.3) loci, including the coding exons, 5’UTR, 3’UTR, and flanking intronic and intergenic sequences in 144 male individuals with ASD obtained from the Autism Genetic Resource Exchange (AGRE) repository. Here, NLGN3 is linked to autism.