Multicolor flow cytometric profiles of mammary epithelial cells have been described extensively in the mouse, but not in the rat. In our study, RMECs showed features similar to those of mice including cell surface expression of CD24 and CD29, defining the luminal and basal populations. The luminal cells showed a CD24+CD29med phenotype and expressed intracellular CK19. Basal cells, the other dominant population in MECs, showed a CD24+CD29hi phenotype and expressed intracellular CK14. A subset of the basal cells, the myoepithelial cells, showed bright staining with phalloidin indicating smooth muscle actin expression. A clear difference WZ8040 between the rat and mouse profiles is that the rat basal population appears to express higher levels of CD29 as compared to the mouse basal population. Subsequently, a distinct population enriched in mammary stem/progenitor cells that has been shown to express higher CD29 levels than the basal cell population in mice, could not be identified in the rat. Another difference between the mouse and rat MEC characterizations is the expression pattern of CD49f and CD61. In the mouse high expression of CD49f has been shown to define the basal population and, together with high expression of CD24, define a MaSC-enriched population. CD61 expressing cells in the mouse mammary gland, together with low expression of CD29, define the luminal progenitor pool. In the rat, expression of both CD49f and CD61 are detectable, but do not separate populations of RMECs, again underscoring interspecies differences in the protein expression profile of the MECs. We followed a previously published study in the rat that used PNL and anti-Thy-1 staining to fractionate the RMECs. That study identified the PNL+ population to be enriched in clonogenic cells, i.e. cells capable of forming alveolar units after transplantation. PNL has also been shown to stain most alveolar epithelial cells and luminal alveolar cells. Here, we verify that the PNL+ and Thy-1+ populations are segregating populations of RMECs. The PNL+ population was found highly enriched in the CD29med population as compared to the CD29hi population, indicating that the clonogenic PNL+ population coincides with the luminal cells, perhaps defining a pool of alveolar progenitor cells, which has been suggested to underlie clonogenicity of a small fraction of the luminal cells in mice. In contrast to the PNL+ population, we found the non-clonogenic Thy-1+ population to equally overlay the CD29med and CD29hi populations. Thy-1 has previously been found to be present on and immediately adjacent to the myoepithelial cells of the ducts and alveoli. As we found SMA expression exclusively in CD29hi cells of the basal RMEC population, we hypothesize that either a myoepithelial cell population defined by Thy-1 can also be found in the luminal population, or Thy-1+ cells define a population other than myoepithelial cells, such as cells of mesenchymal origin as suggested earlier. In this study, we find the luminal population to have a higher percentage of cells in S/G2+M phase of the cell cycle as compared with the basal population.