The aim of the study is to examine rs4680 ("COMT") and rs6265 ("BDNF") as genetic markers of anxiety, ADHD, and tics. Parents and teachers completed a DSM-IV-referenced rating scale for a total sample of 67 children with autism spectrum disorder (ASD). Both "COMT" (p = 0.06) and "BDNF" (p = 0.07) genotypes were marginally significant for teacher ratings of social phobia ([eta]p [superscript 2] = 0.06). Analyses also indicated associations of "BDNF" genotype with parent-rated ADHD (p = 0.01, [eta]p [superscript 2] = 0.10) and teacher-rated tics (p = 0.04; [eta]p [superscript 2] = 0.07). There was also evidence of a possible interaction (p = 0.02, [eta]p [superscript 2] = 0.09) of "BDNF" genotype with "DAT1" 3' VNTR with tic severity. "BDNF" and "COMT" may be biomarkers for phenotypic variation in ASD, but these preliminary findings remain tentative pending replication with larger, independent samples.