This study reports of presence of rab3D, a low M(r) GTP-binding protein, in rat pancreatic acinar cells and islets using a combination of Western blot analysis, two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis/isoelectric focusing, and light and electron microscopic immunocytochemistry. For these purposes, we used an affinity-purified rabbit polyclonal antibody generated against the exclusive amino terminus of rab3D. Failure to detect rab3A, B or C in pancreatic acinar cells with their respective antisera indicated that the rab3D immunoreactivity was not due to cross-reaction with rab3A, B or C. A monoclonal antiserum which recognized rab3A, B, C and D (clone 42.1) detected a second lower M, band in gradient gels. This protein may be an additional member of the rab family. Double label electron microscopic immunogold localizations for rab3D, and the monoclonal antibody that recognizes all members of the rab3 family, showed a preferential localization of rab3D to zymogen granules. In contrast, clone 42.1 detected both zymogen granules and elements of the Golgi complex. Rab3D also localized to the secretory granule field in pancreatic islet cells which additionally expressed rab3A. The majority of rab3D in acinar cells was tightly associated with membrane fractions as indicated by its resistance to alkaline pH extraction. It is likely associated with membranes via isoprenyl groups as suggested by its partitioning into the detergent phase in Triton X-114 extractions. In contrast, bacterially expressed rab3D partitioned solely into the aqueous phase in Triton X-114 extractions. Because of its exclusive location on zymogen granules, rab3D may play a role in regulated exocytosis from pancreatic acinar cells.