Increasing evidence supports the cancer stem cell hypothesis, which postulates that cancer stem cells are responsible for tumor initiation, metastasis, and resistance to treatments. Therefore, they are the cells to target to cure a cancer. To study the behavior of cancer stem cells, markers for prospective isolation of cancer stem cells are crucial. Recently, CD133 has been used extensively as a marker for the identification of stem cells from normal and cancerous tissues. Several more recent studies, however, indicate that CD133 are expressed in differentiated epithelial cells in various organs, and CD133-negative cancer cells can also initiate tumors. The findings suggest that CD133 is not restricted to somatic stem cells and cancer stem cells. However, in many cases CD133 may be used in combination with other markers or methods to acquire stem cells. In this review, we summarize findings in CD133 expression in various tissues and critically discuss its applications in stem cell isolation.