The ras-related Rab3 gene subfamily codes for small GTP-binding proteins which control a late step of exocytosis during which vesicles become docked to the plasma membrane. Rab3a and Rab3b are the most abundant Rab3 isoforms expressed in the CNS of mammals. We have shown previously that the Rab3a protein was selectively distributed and expressed in various regions of the rat brain. Here we have determined the pattern of expression of Rab3b mRNA in the brain and compared it with that of Rab3a mRNA. In addition, we examined the co-expression of these two Rab within individual neurons. In general the Rab3b transcript was detected in many regions which also express Rab3a mRNA but at a lower level than Rab3a, except in the olfactory bulb and in the pituitary where the Rab3b hybridization signal was similar and higher respectively. Double in situ hybridization revealed that Rab3a and Rab3b mRNAs were co-localized in most neurons, in all brain areas examined. However, in each of these areas, subsets of neurons appeared to preferentially express either Rab3b or Rab3a, or some neurons did not express either Rab3 homologue at detectable levels. These data support the view of a functional specialization of Rab3a and Rab3b in the control of exocytosis in neuronal and neuroendocrine cells.