Cancer stem cells have genetic and functional characteristics that can turn them resistant to standard cancer therapeutic targets. Identification of these cells is challenging and is mostly done by detecting the expression of their antigens in a group of stem cells. Currently, there are a significant number of surface markers available which can detect the cancer stem cells by directly targeting their specific antigens present in cells. These markers possess differential expression patterns and sub-localizations in cancer stem cells when compared to non-neoplastic stem cells and somatic cells. In addition to molecular markers, multiple analytical methods and techniques including functional assays, cell sorting, filtration approaches, and xenotransplantation methods are used to identify cancer stem cells. This chapter will overview the functional significance of cancer stem cells, its biological correlations, specific markers, and detection methods.