Substantia nigra pars compacta (SNpc) is highly sensitive to normal aging and selectively degenerates in Parkinson's disease (PD). Until now, molecular mechanisms behind SNpc aging have not been fully investigated using high throughput techniques. Here, we show early signs of aging in SNpc, which are more evident than in ventral tegmental area (VTA), a region adjacent to SNpc but less affected in PD. Aging-associated early changes in transcriptome were investigated comparing late middle-aged (18 months old) to young (2 months old) mice in both SNpc and VTA. A meta-analysis of published microarray studies allowed us to generate a common >transcriptional signature> of the aged (≥ 24 months old) mouse brain. SNpc of late-middle aged mice shared characteristics with the transcriptional signature, suggesting an accelerated aging in SNpc. Age-dependent changes in gene expression specific to SNpc were also observed, which were related to neuronal functions and inflammation. Future studies could greatly help determine the contribution of these changes to SNpc aging. These data help understand the processes underlying SNpc aging and their potential contribution to age-related disorders like PD. © 2013 Gao et al. ; This work was funded by Spanish Ministry of Science and Education, Andalusian Government, and “Marcelino Botín” Foundation. “CIBERNED” (Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas) was funded by the Spanish “Carlos III” Institute of Health. LME was supported by the Spanish “Carlos III” Institute of Health. Support from the Spanish Ministry of Science and Education for MHF (“FPI” predoctoral fellowship) is also acknowledged. ; Peer Reviewed