The concept of cancer stem cell has developed in leukemia. Recently, it has expanded to include solid tumors such as brain or breast tumors. However, the descriptions are not recognized in human gastrointestinal cancers. We used flow cytometry and the DNA-binding dye (Hoechst 33342) to isolate side population (SP) cells from various human gastrointestinal system cancer cell lines. The SP cell fraction is considered to contain abundant stem cells. Fifteen of 16 cancer cell lines from the gastrointestinal system contained 0.3-2.2% SP cells. We studied the characteristics of the SP cells in hepatic or colon cancer cell lines. The results demonstrated that cancers of the gastrointestinal system do contain SP cells that show some characters of so-called stem cells. In this paper, we report our study results with a review of the literature.