Autoradiographic localization of [3H]flunitrazepam in nuclei of the rat cerebral cortex was further confirmed by biochemical analysis of specific nuclear binding. Highly purified rat cerebral cortex nuclei were shown to bind [3H]flunitrazepam specifically. The Kd(app) for nuclear binding was 28 nM for the nuclei compared with a Kd(app) of 1.1 nM for binding of [3H] flunitrazepam to synaptosomal membrane fractions of the same tissue. Inhibition of the nuclear binding with inosine and hypoxanthine was greater than inhibition of the synaptic membrane fractions. These results lead to to conclude that specific binding may occur at both the synaptic membrane and the nuclear levels and that different endogenous ligands may compete at each site for binding. Furthermore, the possibility exists for translocation and alteration of the bound ligand complex from membrane site to nuclear site.