The Autistic Spectrum Disorders (ASD), are known for their considerable heterogenic clinical presentation. Linkage studies have pointed toward very diverse areas of the genome related to the brain and associated with ASD. We hypothesized that small non-coding RNA (ncRNA), like miRNA, siRNA or orphan snoRNAs, could be involved in the pathogenesis of ASD. A group of 73 genes associated with ASD were selected, proven through linkage studies, presence of biological markers (evidence of SNP’s or haplotypes) or candidate genes association studies. A control group of 75 genes, which were predominantly expressed in non-brain tissues was selected. The results showed that the average number of conserved segments per intron in autism specific genes was 3.9, while it was 1.4 in the case of the genes minimally expressed in the brain. A non- parametric statistical test (Mann-Witney) showed a significant difference in degree of conservation between the two groups.