The possibility of identification of cancer stem cells "side population" in solid tumors by using the flow cytometer equipped with 405 nm violet laser was investigated. Ovarian cancer (Skov-3) and colon cancer (Colo 320) cell lines formed the "side population" after vital staining with Hoechst 33342. Analysis of cells isolated from tumor tissue of malignant melanoma and colorectal cancer, also revealed "side population" that was a result of the fluorescent dye exclusion. The percentage of melanoma cells included in the "side population" was the same as that of cells co-expressing cancer stem cells markers - CD34 and CD44. In contrast, the colon cancer "side population" was significantly smaller than the minor populations of colon cancer cells identified by either CD133 expression or exclusion of Rhodamine 123.