The purpose of this study was to identify and localize mucosal epithelial progenitor cells (EPCs) in the rat vagina. Rat vagina was obtained from f77emale Sprague-Dawley rats (12 weeks old, n = 20). To identify EPCs in vagina, we followed a single-cell isolation protocol and analyzed the number of cells staining positive for EPC markers by flow cytometry. The expression of EPC-specific markers (CD44, ERα, PR) was evaluated by immunofluorescence. As shown by confocal immunofluorescence, CD44/ERα double-labeled cells were mainly expressed in the basal cell and suprabasal cell layers. Immunofluorescent staining of CD44 was expressed in the plasma membrane of the vaginal epithelium, and ERα was expressed in the cytoplasm of the vaginal epithelium. The CD44/ERα double-positive cells were noted in the rat vagina by flow cytometric analysis. PR-labeled cells were localized in the intermediate layer of the epithelial space of the vagina. The results revealed the existence of EPCs in the vagina. These findings imply that resident EPCs may have a role in the regeneration of vaginal mucosa.