Animal behaviors are controlled through a complex neural network in the brain. To explore the nature of brain functions, it is critical to investigate the behavioral and physiological roles of specific neuronal types that comprise this network. Immunotoxin (ITX)-mediated cell targeting is a technology designed to eliminate specific cell types that are genetically engineered to express a foreign receptor, utilizing the cytotoxic activity of a recombinant ITX. Lentiviral vectors with highly efficient retrograde gene transfer (HiRet) and neuron-specific retrograde gene transfer (NeuRet) properties are introduced at neuronal terminal regions and transported retrogradely through axons to the cell body, resulting in the transgene expression. HiRet/NeuRet vectors, combined with ITX-mediated cell targeting technology, enable the selective elimination of specific neural pathways within the network, providing an efficient approach for studying the behavioral and physiological roles of target neuronal pathways. This chapter describes a protocol for selective neural pathway targeting and presents an application of this strategy to eliminate striatal input pathways in the mouse brain.