Immunotoxin cell targeting is a transgenic animal technology used to eliminate specific cell types from a complex neural circuitry by using cytotoxic activity of recombinant immunotoxins, which are composed of an antibody variable region fused to bacterial toxin fragments. This technology provides a useful approach for studying the neural circuitry mechanism underlying a variety of brain functions. The present chapter provides a detailed experimental strategy for immunotoxin cell targeting and its application to neural circuitry analysis, in particular focusing on the basal ganglia circuitry, which is implicated in the control of motor functions.