Major progress in understanding epithelial skin stem cells has been accomplished. This has been possible by developing new methods for labeling, tracking, isolating, and characterizing enriched populations of stem cells. This chapter summarizes in vivo and in vitro assays that are currently employed to analyze skin epithelial stem cells. Despite progress, the definition of a stem cell is currently a functional one. Unambiguous identification of a stem cell in intact tissue is still not possible. These limitations hamper molecular studies aimed at unraveling the cellular mechanisms operating in the stem cell compartment. This chapter emphasizes current methods for analyzing hair follicle stem cells, as opposed to other epithelial compartments, because the hair follicle has been most intensively studied up to date.