This protocol describes detailed procedures for rapid labeling of cells in a variety of preparations by means of particle-mediated ballistic (i.e., Gene Gun) delivery of fluorescent dyes. The method has been used for rapid labeling of cells with either lipid- or water-soluble dyes, in a variety of preparations at different ages. Tissue preparations include fixed mouse brain slices (described here), cell cultures, and tissue explants. This ballistic labeling technique is useful for studying neuronal connectivity, function, and pathology in the nervous system of living as well as fixed specimens.