The regenerative potential of mammary epithelium facilitates assessment of the "stemness" of any epithelial subpopulation in transplantation assays. Thus, mammary tissue can be dissociated into single cells, stained for cell surface markers of interest and classified using fluorescence-activated cell sorting. The selected cells can then be transplanted into epithelium-devoided fat pads from recipient hosts. Recent publications have described markers that enrich for mammary repopulating potential. Here, we describe the materials and methods necessary to sort cells according to these markers. This approach can be used interchangeably with other cell surface markers with slight variation to the protocol.