Side population (SP) cells, characterized by their ability to efflux the fluorescent dye Hoechst 33342, were isolated from the small intestine of mice. In the abdominal irradiation model, small intestinal organoid-derived SP (sioSP) cells from ROSA 26 mice were submucosally injected into the small intestinal of the irradiated C57BL/6 mice. In contrast to the control mice, mice receiving sioSP cell transplantation demonstrated far less skin injury. Most importantly, hairs in the irradiated body part of the transplanted mice almost remained black, whereas the counterpart in the control mice almost turned white. Histochemistry studies showed the donor cells gave rise to skin cells in the irradiated skin. Thus, our study demonstrated for the first time that stem cells from the small intestine can differentiate into skin cells under local cues and thus supports the theory of stem cell plasticity.