Caco-2 cells are derived from a human colonic adenocarcinoma, but differentiate into small intestinal-like cells after confluence. While this enterocytic differentiation has been well studied, the presumed parallel loss of colonocyte function has not been as thoroughly examined. To follow the phenotype for both tissues, Western blots were performed using antisera recognizing liver/bone/kidney alkaline phosphatase and surfactant-like particle proteins found in normal human colon, along with antisera against the small bowel representatives of the same proteins. Antisera against proteins enriched in either enterocytes (alpha1-antitrypsin) or colonocytes (surfactant protein A) were also evaluated. Alkaline phosphatase activity increased from 3 to 18 days post-confluence. Activity at 3 days post-confluence derived substantially from both isomers. Thereafter, the colonic (liver/bone/kidney) isomer declined to low levels as the content of the enterocytic isomer rose. A similar pattern was found with colonic (decreasing expression) and enterocytic (increasing expression) surfactant-like particle proteins. In particular, the content of larger enterocytic particle proteins (97 and 116 kDa) increased with time in culture. Expression of alpha1-antitrypsin increased early and remained high, whereas surfactant protein A generally declined after the third day post-confluency. In summary, undifferentiated Caco-2 cells express very low levels of proteins characteristic of either colonocytes or enterocytes. Immediately after confluence, they expressed proteins characteristic of both cell types. Thereafter, the content of colonocyte-specific proteins decreased, whereas those specific for the enterocyte increased. The timing and degree of this phenotypic switch have implications for the interpretation of experiments using Caco-2 cells as a model of small intestinal function.