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ABCG2, CD133 and CD117 are pivotal markers of cancer stem cell, which are involved in carcinogenesis and cancer progression. The expression of these genes has been reported to be associated with the development and progression of many cancers, including non-small cell lung cancer (NSCLC). We selected and genotyped 9 potentially functional single-nucleotide polymorphisms in the 3 genes in a clinical cohort of 1001 NSCLC patients in a Chinese population. We found that variant genotypes of ABCG2 rs3114020 were associated with a significantly increased risk of death for NSCLC (additive model: adjusted hazard ratio = 1.25, 95% confidence intervals = 1.10–1.42, P<0.001). Further stepwise regression analysis suggested that rs3114020 was an independent risk factor for the prognosis of NSCLC. Besides, histology interacted with the genetic effect of rs3114020 in relation to NSCLC survival in the interaction analysis. Our findings show that ABCG2 rs3114020 might be one of the candidate biomarkers for NSCLC survival in this Chinese population, especially among patients with adenocarcinoma.