Thirteen up‐regulated genes and four down‐regulated genes were identified by analysing DEGs between BCSCs and common bladder cancer cell lines. A, The third generation spheres formed by 5637 and T24 cell lines. B, The mRNA expression levels of five stemness‐related regulators (CD133, OCT4, NANOG, ABCB1, ALDH1A1) are extremely up‐regulated in 5637 and T24 cancer stem cells compared to their parental cells. C, In vivo tumourigenesis analysis, 5637‐derived cancer stem cells or parental 5637 cells were subcutaneously injected into nude mice in varying amounts (103, 104, 105, 106 and 107 cells). The tumourigenic ability of 5637 cancer stem cells is extremely enhanced. D, The quality control of the microarray assay. E, The unified standard criterion of the microarray assay. F, Heatmap of the altered gene expression profiles in 5637 CSCs and parental 5637 cells. G, Heatmap of the altered gene expression profiles in T24 CSCs and parental T24 cells. H, Thirteen up‐regulated genes and four down‐regulated genes were identified by intersecting up‐regulated DEGs or down‐regulated DEGs using GCBI (left panel). Gene symbols and accession numbers of selected genes were listed (right panel). I, Heatmap of the altered gene expression profiles of 17 selected genes based on T24 and 5637 related microarray assay