There is increasing evidence of acidification along the entire mammalian collecting duct including the inner medullary collecting duct (IMCD). Recent studies have provided morphologic evidence that the intercalated cells are involved in hydrogen ion secretion in the cortical and outer medullary collecting duct of the rat. In the present study we performed a quantitative and qualitative morphologic examination of the intercalated cells in the IMCD of the rat and compared the results to observations obtained from intercalated cells in the collecting duct in the inner stripe of the outer medulla (OMCDi). Kidneys of male rats were preserved by in vivo perfusion with glutaraldehyde and processed for morphologic evaluation. With light microscopy and scanning electron microscopy intercalated cells were found in the outer third of the IMCD (IMCD1) and accounted for 10% of the total cell population. They were absent in the terminal two-thirds of the IMCD. Examination of the intercalated cells using transmission electron microscopy revealed striking similarities between the cells of the IMCD1 and those in the OMCDi. In addition, no differences were found in the surface densities of the apical or basolateral plasma membranes or the volume densities of the mitochondria of the intercalated cells in the two regions. In light of the morphologic similarity with the intercalated cells of the OMCDi that are believed to be involved in hydrogen ion secretion, it is likely that the intercalated cells of the IMCD1 are also involved in the acidification of tubular fluid.