Parkinson's disease (PD) is characterized by the degeneration of dopaminergic neurons in the substantia nigra (SN) and the subsequent loss of striatal target innervation. Neuroinflammatory responses have been described for virtually all PD cases analysed. Microglia are the resident immune cells of the central nervous system and, thus, are the mediators of neuroinflammation. Approximately 12% of all central nervous system cells are microglia but the distribution and density of microglia differ within distinct brain regions. Interestingly, the SN has been shown to contain more microglia than adjacent structures. We have analysed changes in microglia numbers and in microglial morphology in the postnatal murine nigrostriatal system at various stages ranging from postnatal day 0 (P0) up to 24 months of age. We clearly show that the microglia numbers in the SN and in the striatum dramatically increase from P0 to P15 and significantly decrease in both areas in 18-month-old and 24-month-old animals. Moreover, microglia in the nigrostriatal system of aged mice show signs of dystrophy and degeneration, such as cytoplasmic inclusions, deramification of their processes and membrane blebbing. Our results support the hypothesis of microglial dystrophy during aging in the murine nigrostriatal system, accompanied by subsequent impairment of normal microglial functions. Microglial dysfunction during aging might be a potential risk factor for the development and/or progression of PD.