Tumor stem cells are a small subset of tumor cells with the ability of self-renewal and differentiation and are regarded as a cause of tumor growth and recurrence. Previously we have shown that stem-like label-retaining cells (LRCs) can be detected in nasopharynx, tongue, esophagus and xenograft tumors formed by nasopharyngeal carcinoma (NPC) cell lines (5-8F, 6-10B and TMNE). The present study aimed to identify ABCG2⁺ cells in 5-8F NPC cells and compare their tumorigenic potential with ABCG2⁻ cells, expecting that we can obtain insight into the mechanism of the differential phenotypes of ABCG2⁺ and ABCG2⁻ cells. By using magnetic cell sorting (MACS) method, we isolated ABCG2⁺ cells and ABCG2⁻ cells from 5-8F cells. Among these two subpopulations and unsorted 5-8F cells, the rate of ABCG2⁺ cells at G1 phase was highest, while the rate of ABCG2⁻ cells at S phase was highest, indicating that ABCG2⁺ cells were mostly quiescent. However, ABCG2⁺ cells showed lower cloning efficiency and tumorigenicity than ABCG2⁻ cells. We also used Affymetrix U133 plus 2.0 human whole genome expression chip to identify the gene expression profile of ABCG2⁺ and ABCG2⁻ cells and found that both subpopulations expressed some stem cell associated genes, e.g., PSCA, ABCG2 and ALPI were expressed in ABCG2⁺ cells, and K19, integrin α6, integrin β4, CD44 and K14 were expressed in ABCG2⁻ cells, suggesting there were stem cells in both ABCG2⁺ and ABCG2⁻ cells. Our data demonstrated that there exist ABCG2⁺ cells in NPC cells, but ABCG2 alone is not sufficient for isolating cancer stem cells in 5-8F NPC cells.