Mast cells have previously been identified in mammalian brain by histochemistry and histamine fluorescence, particularly in the rat thalamus and hypothalamus. However, the nature of brain mast cells has continued to be questioned, especially because the electron microscopic appearance often shows secretory granule morphology distinct from that of typical connective tissue mast cells. Here we report that mast cells in the rat hypothalamus, identified based on metachromatic staining with Toluidine Blue, fluoresced after staining with berberine sulfate, indicating the presence of heparin. These cells were also positive immunohistochemically for histamine, as well as for rat mast cell protease I, an enzyme characteristically present in rat connective tissue mast cells. In addition, these same cells showed a very strong signal with in situ hybridization for immunoglobulin E binding protein messenger RNA. However, use of antibodies directed towards immunoglobulin E or its binding protein did not label any cells, which may mean either the binding protein is below the level of detection of the techniques used or that it is not expressed except in pathological conditions when the blood-brain barrier becomes permeable. At the ultrastructural level, perivascular mast cells contained numerous, intact, electron-dense granules which were labeled by gold-labeled anti-rat mast cell protease I. These results clearly demonstrate the presence of perivascular mast cells in the rat hypothalamus, where they may participate in homeostatic processes.