Abstract Nestin is a class VI intermediate filament protein, which was first identified in the early developmental stages of the nervous system. It is widely used as a stem or progenitor cell marker. In the adult mammalian brain, nestin is expressed not only in germinal cells in the neurogenic regions but also in non-germinal cells, such as reactive astrocytes, endothelial cells and pericytes. In the present study, we found another nestin-positive cell type within the adult rat cerebral cortex. We immunohistochemically analyzed which types of cells exhibit immunoreactivity for nestin, and through the use of co-immunostaining with Iba1, CD11b and GLUT5, which are known to be specific for microglia, identified these cells as microglia. Approximately > 20% of the microglia were immunoreactive for nestin in the rat cerebral cortex under normal conditions. Nestin signals were not widely distributed in the microglial cytoplasm, but were restricted to the perikaryon and to parts of the cell processes. Nestin-positive microglia were also immunoreactive for the intermediate filament protein vimentin. These observations demonstrate that a subpopulation of microglia in a resting state has nestin-containing intermediate filament networks. Therefore, nestin in conjunction with vimentin might have roles in maintaining the structural integrity of the microglia.