Ionizing radiation (IR) began to be a powerful medical modality soon after Wilhelm Röntgen’s discovery of X-rays in 1895. Today about 60% of cancer patients worldwide receive radiotherapy in their course of cancer control. In the past decades, the technology for precisely delivering tumor IR dose such as stereotactic body radiation therapy (SBRT) has been significantly enhanced, which increases the overall local tumor response and clinical benefit. However, in achieving the goal for long-term cancer control, radiotherapy (RT) has faced several major challenges including the elucidation of the microenvironment causing tumor repopulation and resistance, especially with the most aggressive tumor cells in late phase metastatic lesions. To meet this challenge, a great deal of effort has been devoted to revealing not only the mechanistic insight of tumor heterogeneity, but also the emerging complexity of the irradiated microenvironment. Such new knowledge provides the explanation for the long recognized tumor heterogeneity and tumor cell repopulation, one the major "R"s in tumor radiobiology, which involves cancer stem cells (also termed tumor-imitating cells, cancer stem-like cells, or stem like cancer cells). It is generally accepted that CSCs plays a key role in tumor adaptive radioresistance and are involved in clinical tumor response. The specific cell surface biomarkers as well as the biological topographies of CSCs in many solid tumors have been identified; some of them overlap with those detected in normal stem cells. However, the exact molecular mechanism causing the radioresistant phenotype of CSCs, especially the dynamic nature of CSCs themselves under RT and their communication with the irradiated tumor microenvironment including stromal cells and immune cells, remains to be elucidated. Further elucidation of the complexity of the irradiated local tumor microenvironment in which CSCs reside may generate significant new information to resensitize radioresistant tumor cells and thus to improve therapeutic efficacy. In this chapter, I will describe the general information on normal stem cells, CSCs, CSCs-associated tumor repopulation and energy reprogramming and potential therapeutic targets. The dynamic features of radioresistance-associated factors such as NF-κB and HER2 in some CSCs including breast cancer and GBM will be discussed.