Intercalated cells are present in both the collecting duct, which is derived from the ureteric bud, and the connecting tubule (CNT), which is part of the nephron and thus is developed from the metanephric blastema. However, the embryologic origin of the intercalated cells has not been established. Two populations of intercalated cells, type A and type B, exist in the CNT and the cortical collecting duct (CCD). It is uncertain, however, whether these cells represent truly distinct cell types or whether one is derived from the other. In this study we have used specific antibodies to carbonic anhydrase II (CA II), H(+)-adenosinetriphosphatase (H(+)-ATPase), and band 3 protein to identify subpopulations of intercalated cells, to determine the site and time of their appearance, and to follow their differentiation in the developing rat kidney. Prenatal kidneys from 16-, 17-, 18-, and 20-day-old fetuses, and postnatal kidneys from 0-, 3-, 7-, 14-, and 21-day-old pups were preserved for immunohistochemical studies. Immunostaining for CA II and H(+)-ATPase appeared simultaneously in a subpopulation of cells in the CNT and the medullary collecting duct (MCD) of the 18-day-old fetus, suggesting that intercalated cells differentiate from separate foci, one in the nephron and one in the collecting duct. Cells with apical and cells with basolateral labeling for H(+)-ATPase appeared in the CNT and MCD at 18 days of gestation, indicating that type A and type B cells differentiate simultaneously during renal development. Band 3 immunostaining was very weak in the fetal kidney, but a striking increase in labeling was observed in the 3-day-old kidney, suggesting that there is an activation of acid-secreting cells shortly after birth. In the fetal kidney, immunostaining for CA II and H(+)-ATPase was observed in cells throughout the MCD and on the papillary surface. After birth, immunostaining gradually disappeared from both the papillary surface and the terminal inner MCD, and cells with basolateral labeling for H(+)-ATPase gradually disappeared from the outer MCD. The results of this study suggest that type A and type B intercalated cells represent distinct cell types that derive from undifferentiated cells at two separate foci, one in the nephron and one in the collecting duct. Our results also suggest that entire populations of intercalated cells are eliminated from the collecting duct during normal renal development.