Bladder cancer stem (initiating) cell has not been isolated now, and no one verified its persistence experimentally. The aim of this study was to conclude the persistence of bladder cancer stem (initiating) cell in human primary bladder cancer and investigate the possibility of EMA(-) CD44v6(+) as markers of bladder cancer stem (initiating) cell. Genes differentially expressed between normal urothelium and low malignant bladder cancer were identified by DNA array assay. Overpressed stem cell related genes, Bmi-1 and EZH2, were verified by immunohistochemistry. Side population cells in bladder cancer were found under fluorescence microscope. The value of 28 potential surface markers of bladder cancer stem (initiating) cell for isolating them were judged by immunohistochemistry. Both EMA(-) and CD44v6(+) cells located in basal layer (potential location of stem cells). After gathering the CD44v6(+) cells and EMA(-) cells by magnetic cell sorting, their ability for colony-forming, self-renewal and extensive proliferation were assayed by cells culture. Both EMA(-) cells and CD44v6(+) cells posses the ability for colony-forming, self-renewal and proliferation. We conclude the persistence of bladder cancer stem (initiating) cell. Bladder cancer stem (initiating) cell might be among EMA(-) CD44v6(+) subset. Our strategies for isolating bladder cancer stem (initiating) cell might be useful for isolating other undetermined epithelial cancer stem cell, especially those in well-differentiated cancers.