Structurally and functionally distinct populations of intercalated cells have been described in the collecting duct of both rat and rabbit. However, little is known about these cells in the mouse kidney. The study presented here examines ultrastructural and immunological characteristics of different types of intercalated cells in the mouse. Kidneys of two strains of normal female mice, C57BL/6 and IBR, were preserved by in vivo perfusion with 1% glutaraldehyde or paraformaldehyde-picric acid fixatives and processed for morphological evaluation or light and electron microscopic immunohistochemistry, respectively. The avidin-biotin-horseradish peroxidase procedure was performed on was sections using antibodies against carbonic anhydrase II, H+ -ATPase and Band 3 protein. Immunogold cytochemistry was performed on Lowicryl sections using antibodies to H+ -ATPase and Band 3 protein. Colocalization of H+ -ATPase and Band 3 protein was performed by double labeling using an immunogold technique with silver enhancement. Intercalated cells identified by positive staining for H+ -ATPase and carbonic anhydrase II constituted 35% to 40% of all cells in the connecting tubule (CNT), cortical collecting duct (CCD), and outer medullary collecting duct (OMCD). Type A intercalated cells identified by positive Band 3 staining constituted 16%, 24%, and 33% of the total cell population in the CNT, CCD, and OMCD, respectively. Electron microscopy and immunogold cytochemistry demonstrated three distinct populations of intercalated cells. Type A intercalated cells with apical H+ -ATPase and basolateral Band 3 immunoreactivity were present in all segments examined, and had prominent apical microprojections and characteristic tubulovesicular structures beneath the apical surface, both coated with studs on the cytoplasmic face. Type B intercalated cells with basolateral and cytoplasmic H+-ATPase and no Band 3 immunoreactivity were most frequently observed in the initial collecting tubule, but were present also in the CNT and early CCD. Type B intercalated cells had a fairly smooth apical surface, a gray zone free of organelles beneath the apical plasma membrane, and small cytoplasmic vesicles without studs throughout the cell. A third type of intercalated cell with apical and cytoplasmic H+-ATPase, but no basolateral Band 3 protein, was observed exclusively in the CNT and the initial collecting tubule. This type of cell was large, with numerous mitochondria, and vesicles coated with studs were present throughout the cell. It resembled a third type of intercalated cell described previously in the rat. It is concluded that three morphologically and immunologically distinct types of intercalated cells are present in the mouse kidney.