VAMPs are synaptic vesicle-specific proteins composed of a carboxy-terminal hydrophobic membrane anchor and an approximately 100 amino acid domain oriented towards the cytoplasm. In rat, two 77% homologous VAMP genes are expressed in the CNS. To precisely localize the neurons expressing these 2 forms of VAMP, we have used RNA blotting and in situ hybridization histochemistry with RNA probes specific for the 3' untranslated regions of the transcripts. These experiments revealed that the 2 genes are expressed in distict, but slightly overlapping, patterns in the rat brain. VAMP-1 expression is localized to a limited number of nuclei, particularly those involved in modulating somatomotor functions, while VAMP-2 expression is more ubiquitous, being found in nuclei associated with autonomic, sensory, and integrative roles. These data suggest that the specific structural features of individual VAMPs may play an important role in synaptic vesicle metabolism.