The radiation inactivation technique has been used to estimate the molecular weights of 5-HT binding sites in various regions of the rat brain. Using 3H-5-HT or 3H-8-OH-DPAT as the ligand, the same molecular weight of 55,000-60,000 daltons was calculated for the postsynaptic 5-HT1A and 5-HT1B sites in the hippocampus and cerebral cortex. Studies with 3H-ketanserin as the selective ligand indicated a molecular weight in the same range for the post-synaptic 5-HT2 binding site in the cerebral cortex. In contrast, a higher value (67,000 daltons) was found for the presynaptic 5-HT3 site selectively labelled by 3H-8-OH-DPAT in the striatum and cerebral cortex. The curvilinear pattern of the radiation-induced inactivation of 5-HT1A and 5-HT1B binding sites suggested that both sites belong to complex polymeric structures. In contrast, the 5-HT2 and 5-HT3 sites may correspond to less cooperative structures since simple monoexponential inactivation curves were observed upon irradiation.