We used next-generation sequencing to generate a comprehensive catalog of transcriptional changes that occur in response to cocaine treatment and withdrawal in the primary reward center of the brain. Pathway analysis enabled the complete categorization of transcriptional changes in signaling pathways known to be important in addiction along with the identification of pathways not previously considered important. These data should serve as a resource for development of new targets for cocaine therapy and facilitate selection of protein interaction and pathway targets for future study. With more information about their normal physiological roles, the extracellular domains of the many cadherins and protocadherins that respond to cocaine may be useful therapeutic targets. Pharmaceutical cocktails targeted to a subset of the specific GPCRs whose expression is altered during withdrawal may prove to be more effective than treatments targeting a single pathway.