Stereotaxic injection is an attractive approach for studying genetic, cellular and circuit functions in the brain. Injection of anatomical tracers, site-targeted lesions and gene delivery by recombinant adeno-associated viruses and lentiviruses in mice are powerful tools to study nervous system development and disease mechanisms. Stereotaxic injection of LPS or 6-hydroxydopamine has been used to establish animal models of Parkinson’s disease, the most common neurodegenerative movement disorder. Importantly, this protocol allows the manipulation of gene expression in the targeted rodent brain regions and even targeted cell types or a subpopulation of cells in the injected region at any postnatal developmental stage up to adulthood.