Here we conducted the first unbiased transcriptomic analysis of post-mortem tissue from OFC and striatum in OCD and unaffected comparison subjects. We found significantly lower expression of transcripts associated with synaptic neurotransmission across all regions and determined that these changes may be strongest in medium spiny neurons in the caudate nucleus and nucleus accumbens. Further examination of these data could help identify novel treatment targets for OCD and related disorders and will serve as a foundation for future larger studies.