Cancer stem cells in various tumors have been isolated by antigenic markers on cell surface or functional markers for cancer stem cells. The purpose of this study is explore if the expression of CD133, known as surface marker for common cancer stem cells, is related to the expression of ABCG2, known as the functional marker for stem cells in various cancer cell lines. We determined the expression of CD133 and ABCG2 in the established human gastric cancer cell line (SNU216), hepatoblastoma cell line (HepG2), colon cancer cell line (SNU1040), and brain tumor cell line (A172). SNU 216 and SNU 1040 cells showed a higher level of CD133 expression, whereas HepG2 and A172 cells expressed almost undetectable level of CD133. However the expression level of ABCG2 was higher in HepG2 and A172 cells than in SNU 216 and SNU 1040 cells. 5-FU treatment increased both of the CD133 and ABCG2 expression in SNU216 and SNU1040 cells, but not in HepG2 and A172. The expression of ABCG2 in CD133 positive population of SNU1040 and A172 cells was higher than in CD133 negative population. This study showed there is a relationship between CD133 and ABCG2 expression in some cancer cell lines but not in all. CD133 positive cells expressing ABCG2 in a high level may be more resistant to anti-cancer drug, which suggest that CD133 might be a useful marker to isolate cancer stem cells having a resistance to anti-cancer-drug.