Evidence is emerging that the mouse mammary epithelium is arranged as a hierarchy that spans from stem cells to lineage-restricted progenitor cells to differentiated luminal and myoepithelial cells. The use of fluorescence-activated cell sorting (FACS) in combination with quantitative functional clonal assays represents a powerful tool for studying the properties of mouse mammary stem and progenitor cells. This chapter outlines the experimental procedures for generating single viable cell suspensions of mouse mammary epithelial cells, immunostaining cells for flow cytometry, in vitro assays for the detection and enumeration of mouse mammary progenitor cells, and in vivo assays for the detection and enumeration of mouse mammary stem cells.