Animal models can help determine the etiology of neurodegenerative diseases such as Parkinson’s disease. Here, we conducted transcriptome analysis of the rotenone model of Parkinson’s disease in rats. Exposure of 9-week-old Wistar rats to rotenone at 3 mg/kg/day for 14 days reduced spontaneous motor activity to 49% of that of control rats. Immunohistochemical analysis revealed increased expression of major histocompatibility complex (MHC) molecules in the substantia nigra of rotenonetreated rats, which was deduced by DNA array analysis. Further, gene set enrichment analysis of the transcriptome extracted the presence of a cytokine network, which included TNF-α. The expression of these proteins tended to be reduced at developed states of the disease. Thus, our analyses of the rotenone rat model still provides new insights into the etiology of Parkinson’s disease.