Obsessive compulsive disorder (OCD) is observed at increased rates in first-degree relatives of probands with autism spectrum disorders (ASDs). In addition, OCD-like traits are observed in autism, and in Asperger syndrome. Furthermore, subjects with OCD may have traits that overlap with some aspects of higher functioning ASDs. These observations suggest that OCD and ASDs may share some genetic risk factors. In support of this, it has recently been suggested that both common and rare functional variants in the serotonin transporter (SLC6A4) may increase risk for OCD and/or ASD. We will review our large-scale analysis of common and rare functional variants SLC6A4 in ASDs and relate these results to studies of OCD. In parallel studies, we have carried our linkage analysis in families with ASDs, focusing on those with more severe OCD-like traits. These families demonstrated increased evidence for linkage to chromosomes 1, 6, and 19. Evidence for linkage to chromosomes 6 and 19 have been observed in other studies, which we will summarize. Finally, we have examined the evidence that common variants in the NrCAM, TPH1 and TPH2 genes are associated with ASDs, particularly in patients with more severe OCD-like traits, and these results will be summarized.