The mouse skin is composed of at least three differentiating epithelial compartments: the epidermis, the hair follicle, and the associated glands such as the sebaceous glands. Proliferation of these epithelial cells takes place in the keratinocytes' layer or basal cell layer; in the periphery of the sebaceous gland (the basal layer of the gland) and in specific cell compartments around the hair follicle. In mouse skin, an epithelial stem cell population is thought to localize to the bulge region of the hair follicle, a segment that does not undergo regression during the hair cycle. In addition, several other putative stem cells and/or progenitors have been identified in different regions of the hair follicle. Using the Hoeschst exclusion technique, originally described in the hematopoietic system, it has been possible to isolate a mouse keratinocyte cell population with characteristics of stem cells (side-population, SP). One of the main features of these SP is their ability to efflux antimitotic drugs as well as some specific dyes. This characteristic allows for SP cells to be isolated based upon their capacity to efflux the dye Hoechst 33342, through a mechanism driven by a membrane transporter, the breast cancer resistance protein (BCRP1/ABCG2). In this chapter, we described the isolation of SP stem cells from adult mouse hair follicles utilizing the Hoeschst exclusion technique by flow cytometry analysis.