Using clonal and population analysis, we found that the MCF7 and SK-OV3 were composed mainly of cancer stem cells. Together with SP analysis, we found that both SP and NSP cells of MCF7 and SK-OV3 contained different proportions of cancer stem cells. In addition, we discovered that MCF7 SP cells were able to generate non-SP cells, and conversely non-SP cells generated SP cells; Moreover, we showed that Hoechst 33342 and FACS were harmful to the clonogenicity of MCF7 and SK-OV3 cells. (C) 2007 Elsevier Inc. All rights reserved.