OBJECTIVE: Autism spectrum disorder (ASD) and attention deficit/hyperactivity disorder (ADHD) are developmental disorders that overlap in a number of domains, sometimes complicating clinical distinction between both disorders. Although there is some evidence for a genetic overlap, there are no reports on genes that could differentiate between ASD and ADHD. Furthermore, it is not known whether this genetic overlap is influenced by co-morbid substance use disorders (SUD). METHODS: A total of 110 adult patients with ASD (n=61) or ADHD (n=49) with or without a lifetime history of SUD participated in a study in which we genotyped polymorphisms in five known candidate genes for (one of) the disorders, i.e. the 5HTTLPR in SLC6A4/5-HTT, rs1800497 (TaqIA C>T) in DRD2, rs7794745 in CNTNAP2, rs1843809 in TPH2, and rs6565113 in CDH13. Genotyping was by Taqman-based analysis or by simple sequence length analysis, where appropriate. RESULTS: ASD could be differentiated from ADHD with nominal statistical significance by the 5HTTLPR, and the polymorphisms in TPH2 and CNTNAP2. The results were independent of lifetime SUD status. CONCLUSIONS: Serotonergic genes could prove to play an important role in differentiating between ASD and ADHD, but the results of this exploratory study need replication.