The identification of neuronal circuits and their specific functions in behavior and disease is essential for understanding the mammalian brain. A promising technique to advance this goal involves the use of lentiviral vectors for specific gene transfer into specific brain circuit. The vesicular stomatitis virus glycoprotein (VSV-G) pseudotyped lentiviral vectors can introduce genes in neurons at the injection sites. Retrograde lentiviral vectors, such as highly efficient retrograde gene transfer (HiRet) and neuron-specific retrograde gene transfer (NeuRet) vectors, enable the delivery of genetic materials into neurons based on their axonal projections. These lentiviral vectors represent a powerful genetic tool for neuroscience research. Here, we describe a step-by-step experimental procedure for injecting viral vectors into target brain areas using the basal ganglia circuit as example in mice to map their functional properties. This methodology, which integrates local and retrograde gene transfer with optogenetic manipulation, offers a robust framework for investigating the functional organization of neuronal circuits. In demonstrating this approach, this chapter aims to guide researchers to apply these techniques to study brain functions and disorders of interest.