Side population (SP) cells may play an important role in tumorigenesis and cancer therapy. We isolate and identify the cancer stem-like cells in human esophageal carcinoma (EC) cell lines, EC9706 and EC109 cells labeled with Hoechst 33342. Both the cell lines contained SP cells, and the cells that had the strongest dye efflux activity ("Tip"-SP cell) in EC9706 had higher clone formation efficiency than non-SP cells. When transplanted into nonobese diabetic/severe combined immunodeficiency (NOD/SCID) mice, "Tip"-SP cells showed at least 50 times higher tumorigenicity than non-SP cells. Microarray analysis discriminated a differential gene expression profile between "Tip"-SP and non-SP cells, which is further tested using quantitative real-time RT-PCR. It is ascertained that several important stem cell-related genes (including OCT-4, SOX-2, BMI-1, and ZFX), two ATP-binding cassette (ABC) transporter genes (ABCG2 and ABCA5), and three Wnt and two Notch signal pathway-related genes (such as FZD10, PTGS2, KLF5, TTK, and RBM15) were upregulated in "Tip"-SP cells. Western blot showed a higher expression of beta-catenin protein in "Tip"-SP cells. All these indicated that the minority population described as "Tip"-SP cells possessed cancer stem cell character. Further understanding of tumor stem cell-specific traits will offer insights on the early stages of tumorigenesis for prevention and enhanced selectivity of antitumor therapeutics.