Synaptotagmin IX has been postulated to function as a major Ca2+ sensor for dense-core vesicle exocytosis in neuroendocrine cells. In this study, we investigated the subcellular localization and developmental expression profile of synaptotagmin IX in the mouse brain and found that it is mainly present in the dense-core vesicle fraction, which is devoid of synaptotagmin I and synaptophysin. We also found that the synaptotagmin IX expression level is constant throughout the postnatal development of the mouse brain, whereas the synaptotagmins I, II, III, VI, and XII are upregulated in parallel with synaptogenesis. These findings suggest that synaptotagmin IX regulates the transport of certain vesicles in the brain other than synaptic vesicles.