Cancer stem cells (CSCs) are considered to be a population of tumor cells, which are responsible for tumor initiation and progression. They are also involved in metastasizing and may be a possible cause of multidrug resistance and tumor recurrence. CSCs possess the ability to self- renew and show a tumorigenic potential. Functional assays, which enable the detection of these properties, represent the main tool for identification of CSCs. This article summarizes both in vitro and in vivo methods used to identify the CSCs with emphasis on recently employed techniques of CSCs detection. In vivo tumorigenicity assay, sphere formation assay and colony- forming unit assay belong to the most commonly used functional assays. Further, label- retention assay and aldehyde dehydrogenase activity assay are described in this article.