Cancer stem cells have been isolated from human gliomas and many other parenchymal tumors. It was previously assumed that many established malignant cell lines also contain a rare subpopulation of stem cells. This study was designed to investigate the fraction of cancer stem cells in the C6 glioma cell line using clonal and population analyses, rather than isolating methods, which are based on specific markers. Interestingly, in the serum-containing medium, each of the 67 single C6 cells plated per miniwell was able to generate a clone and subclones, which subsequently gave rise to a xenograft glioma in the BALB/C-nude mouse. The CD133- C6 cells also possessed clonogenic, self-renewal, and tumorigenic capacities. Moreover, our findings indicated that brief exposure to Hoechst 33342 was harmful to the clonogenicity and proliferation of individual C6 cells. Therefore, the non-side-population cells may be deprived of their stem cell features in the process of Hoechst 33342 staining as a step in isolating a Hoechst-negative side population with flow cytometry. Thus, we concluded that the C6 line was mainly composed of cancer stem cells, although many of them were neither CD133+ nor side population.