Numerous studies have demonstrated the presence of cancer stem cells (CSCs) within solid tumors. Although the precursor of these cells is not clearly established, recent studies suggest that the phenotype of CSCs may be quite plastic and associated with the epithelial-to-mesenchymal transition (EMT). In patients, the presence of EMT and CSCs has been implicated in increased resistance to radiotherapy. Hypoxia, a negative prognostic factor for treatment success, is a potent driver of a multitude of molecular signalling pathways that allow cells to survive and thrive in the hostile tumor microenvironment and can induce EMT. Hypoxia also provides tumor cells with cues for maintenance of a stem-like state and may help to drive the linkage between EMT and CSCs. Understanding the biology of CSCs, the EMT phenotype and their implications in therapeutic relapse may provide crucial new approaches in the development of improved therapeutic strategies.