Zinc transporter-3 (ZnT-3), a member of a growing family of mammalian zinc transporters, is expressed in regions of the brain that are rich in histochemically reactive zinc (as revealed by the Timm's stain), including entorhinal cortex, amygdala, and hippocampus. ZnT-3 protein is most abundant in the zinc-enriched mossy fibers that project from the dentate granule cells to hilar and CA3 pyramidal neurons. We show here by electron microscopy that ZnT-3 decorates the membranes of all clear, small, round synaptic vesicles (SVs) in the mossy fiber boutons of both mouse and monkey. Furthermore, up to 60-80% of these SVs contain Timm'sstainable zinc. The coincidence of ZnT-3 on the membranes of SVs that accumulate zinc, and its homology with known zinc transporters, suggest that ZnT-3 is responsible for the transport of zinc into SVs, and hence for the ability of these neurons to release zinc upon excitation.Most of the zinc in the mammalian brain is associated with metalloproteins; however, there is also a pool of histochemically reactive zinc that exists in synaptic vesicles (SVs) of a subset of glutamatergic neurons, which has led to classification of these neurons as zinc-containing or zinc-ergic (1-4). Pathways utilizing this vesicular form of zinc have been mapped using histochemical stains such as the neo-Timm's sulfidesilver method (5), selenium stain (6, 7), and the fluorescent compound, TSQ (8). One of the best described zinc-ergic systems is found in the rodent hippocampal formation, where vesicular zinc can be detected in each component of the trisynaptic circuit that includes (i) perforant path projections from the entorhinal cortex to the outer molecular layer of the dentate gyrus, (ii) mossy fiber (MF) projections from granule cells in the dentate gyrus to hilar neurons and pyramidal cells in the CA3 region (4, 9-11), (iii) projections from CA3 pyramidal neurons to neurons in the CA1 region, and (iv) projections from CA1 to subiculum (3, 4). Electron microscopy (EM) has revealed that the Timm's stain precipitate is present within SVs in the giant axonal boutons of the MFs in the hilus and stratum (s.) lucidum (1, 2, 12). However, only Ϸ10-15% of the SVs within a given bouton have been shown to contain Timm's precipitate (2); thus, it has been difficult to ascertain whether zinc is present in a subset of vesicles or if it is present in the same vesicles as glutamate.Accumulation of zinc within SVs presumably depends on the action of specific transporters, by analogy with the accumulation of other neurotransmitters in SVs (13). A gene, designated zinc transporter-3 (ZnT3), homologous to two established zinc transporters (14, 15) was recently cloned (16). ZnT-3 was shown by in situ hybridization to be expressed at high levels in hippocampus and neocortex. Immunocytochemical studies demonstrated its localization to the MFs, where the histochemical Timm's reaction has revealed zinc-containing SVs. This profile suggested that ZnT-3 might be the vesicular zinc transporter responsible for sequestration ...