Alkaline phosphatase (ALP) is known to be expressed in the several somatic stem cells and cancer cells. To investigate whether ALP may be a promising marker for cancer stem cells (CSCs), we examined the expression of ALP in human squamous cell carcinoma HeLa cells using a cytochemical Advances in Stem Cells 2 staining kit. We found that approximately 40% of HeLa cells were positive for ALP activity. A single cell-derived colony assay revealed that the newly formed colonies could be classified into uniformly (U, 23%), mosaically (M, 17%), and non-stained (N, 60%) colonies. Each colony was picked and cultured for 2 additional weeks for cell propagation; the cells were either M-(45%) or N-type (55%), suggesting that the U-type colonies may have spontaneously changed to M-type colonies during cultivation. These resulting M-or N-type cells were stable with respect to ALP activity. DNA microarray analysis revealed that the gene expression pattern of N-type cells is almost identical to that of their parental HeLa cells (comprising M-type cells), but several genes including ALP gene were upregulated in the HeLa cells. Cultivation of single HeLa cell-derived colonies in the presence of the small molecule 6-bromoindirubin-3'-oxime (BIO), a potent inhibitor of glycogen synthase kinase 3 (GSK3), caused a reduction in the ratio of M-type colonies, suggesting that the transition from U-to M-type colonies is regulated by the Wnt/β-catenin signaling pathway. Although there is no evidence, at present, that the ALP-positive cells are CSCs, future investigation may reveal that HeLa cells may be a good model for CSC study.