Cancer stem cells are one of the most promising targets for cancer treatment. In head and neck cancer, CD44 has been regarded as a cancer stem cell marker. However, apart from the standard CD44 (CD44s), many other variants of CD44 exist, and their specific roles are still unknown. Radiation resistance is a known characteristic of cancer stem cells. Therefore, we irradiated five head and neck squamous cell carcinoma cell lines and investigated whether the expression patterns of CD44 variants changed. Common results showed that the number of CD44s-positive cells decreased and that of CD44 variant 9 (CD44v9)-positive cells increased. This suggested that CD44v9 is useful as a marker for cancer stem cells and may be a target for therapy.