Synaptotagmin is known to be a major membrane protein of synaptic vesicles (SVs) in neurons. We have now used an immunoisolation procedure to demonstrate that synaptotagmin is also present in the membranes of peptide containing large dense-core vesicles (LDCVs) of rat hypothalamus and bovine posterior pituitary. Synaptotagmin bead- immunoisolated organelles from these tissues primarily consisted of SVs but contained occasionally larger structures reminiscent of LDCVs that were absent from vesicle populations immunoisolated with a synaptophysin antibody. Furthermore, the vesicles immunoisolated with synaptotagmin beads contained significant amounts of neuropeptide Y (NPY). In contrast, vesicles immunoisolated with synaptophysin beads did not contain detectable levels of NPY. Sucrose density gradient fractionation of postnuclear supernatants obtained from the bovine posterior pituitary resulted in a bimodal distribution of synaptotagmin, corresponding to the positions of both SVs and neurosecretory granules. A similar distribution was found for cytochrome b561 and the 116 kDa subunit of the vacuolar proton pump. In contrast, the SV proteins synaptophysin, SV2, and p29 were restricted to the SV-containing fractions. Immunoisolation of small and large vesicles from the sucrose gradient confirmed the differential distribution of synaptotagmin and synaptophysin in the two types of secretory vesicles in nerve endings of the posterior pituitary. We conclude that synaptotagmin is a constituent of both SVs and peptide- containing secretory vesicles in the nervous system. Since both types of organelles undergo Ca(2+)-dependent exocytosis, these findings support a general role of synaptotagmin as an exocytotic Ca2+ receptor.