ObjectiveTo study the activities of different gene promoters in colon cancer stem cells and to search for effective promoter for targeted therapy of colon cancer stem cells. MethodsCD133+CD44+ cells were sorted from cell line HCT116 by flow cytometry. Nanog, Muc1 and Survivin gene promoters were amplified by PCR and were separately cloned into pGL3-basic plasmid. pGL3-basic-promoter plasmid or pGL3-basic-control plasmid together with plasmid pRL-sv40 were co-transfected into colon cancer cell lines (HCT116,SW620, and HT29), CD133+CD44+ HCT116 cells, and normal human liver cell line QSG7701. And then promoter activity was examined by dual-luciferase assays. ResultsThe constructed pGL3-basic-Nanog, pGL3-basic-Muc1 and pGL3-basic-Survivin were confirmed correct by sequencing. We found that 42.2% of HCT116 cells were CD133+CD44+ cells. Dual-luciferase activity detection showed that Muc1 and Survivin promoters had strong activities in both colon cancer cells and CD133+CD44+ HCT116 cells, and they had low activities in normal cells QSG7701. ConclusionSurvivin and Muc1 promoters may serve as effective candidate for targeted treatment of colon cancer stem cells.