The design, development and use of small molecule fluorescent ligands to directly or indirectly study receptors,enzymes and other targets in the central nervous system (CNS) have in the recent years become an intense area of investigation, especially for use in quantitative, sensitive and direct binding assays to study target proteins, both intra- and extra-cellularly and as prodromal diagnostic tools. The rapid development of ultra sensitive fluorescent spectroscopic approaches, such as fluorescence correlation spectroscopy, flow cytometry, confocal laser scanning microscopy,fluorescence polarization and multi-photon fluorescence microscopy, is opening new scenarios for the use of small molecule fluorescent ligands in the study of CNS pharmacology. In combination with effective and efficient labeling protocols, these techniques offer enormous possibilities at both micro- and nanometer level to develop parallel multifaceted tools in pharmacological and related sciences. This review covers small molecule fluorescent ligands that have been applied to study proteins and other targets in the CNS through visualization by means of fluorescent imaging technologies.