The identification and characterization of esophageal stem cells are critical to our understanding of the biology of the esophageal epithelium in health and disease. However, the proliferative compartment within the mouse esophageal epithelium remains poorly characterized. Here, we report that the basal cells of the mouse esophagus can be separated into three phenotypically and functionally distinct subpopulations based on the expression of alpha(6) integrin and transferrin receptor (CD71). Cells that express high levels of alpha(6) integrin and low levels of CD71, termed alpha(6)(bri)CD71(dim), are a minor subpopulation of small and undifferentiated cells that are enriched for label-retaining cells and thus represent a putative esophageal stem cell population. Conversely, cells expressing high levels of both alpha(6) integrin and CD71 (alpha(6)(bri)CD71(bri)), the majority of basal esophageal cells, are enriched for actively cycling cells and therefore represent a transit-amplifying population. Kinetic analyses revealed that a third cell population, which is alpha(6) integrin-dim and CD71-bright (alpha(6)(dim)), is destined to leave the basal layer and differentiate.