Present evidence suggests that in the small intestine, villus cells are primarily absorptive and crypt cells are primarily secretory. In order to further confirm that there are differences in transport properties between villus and crypt cells, we have separated villus from crypt cells, using calcium chelations techniques, and determined the distribution of Na:H and Cl:HCO3 exchange activity on brush border membrane and basolateral membrane preparations from these two cell populations. Separation of cells was determined utilizing alkaline phosphatase and maltase activity as a marker of villus cells and thymidine kinase activity as a marker of crypt cells. Utilizing these techniques, we were able to sequentially collect cells along the villus-crypt axis. Na-stimulated glucose and alanine uptake in brush border membrane vesicles diminished from the villus to the crypt region in the sequentially collected cells fractions, further suggesting separation of these cells. Brush border and basolateral membranes were then prepared from cells from the villus and crypt areas, utilizing a continuous sucrose gradient. In the villus cells, Na:H exchange activity was found associated with both the brush border and basolateral membrane, whereas, in crypt cells, Na:H exchange activity was only found on the basolateral membrane. Cl:HCO3 exchange activity was found only on the brush border membrane, in both villus and crypt cells. These studies suggest functional heterogeneity in ion transport between villus and crypt cells.