In this study, we investigated the expressions of Lgr5, Oct4, CD133, EpCAM, CD54 and Sox2 through IHC and qPCR in GC tissues. In IHC, multivariate analyses demonstrated that Lgr5, CD133 and EpCAM were independently related to old age, CD133 and Sox2 were independently associated with well or moderate differentiation, while Oct4, CD133 and EpCAM were independently related to tumor progression. Regarding qPCR, logistic regression analyses showed that Lgr5 and Sox2 were independently related to well or moderate differentiation and young age, respectively. With respect to prognosis in IHC, we only found that the patients with high expression of Oct4 and EpCAM had significantly worse survival outcomes than those with low expression in univariate analyses. The differences between the high and low expression groups of other four markers were not significant. However, none of these six markers were independent prognostic factors. Based on the differences in survival outcomes between the patients in high and low expression of Oct4 and EpCAM, we combined Oct4 and EpCAM together to investigate the survival outcomes between low expression of Oct4-EpCAM and high expression of Oct4/EpCAM (control group). Cox regression showed that Oct4-EpCAM was the independent prognostic factor. In qPCR, we only found that CD133 was an independent prognostic factor, indicating that the patients with CD133 high expression had significantly worse prognosis than those with CD133 low expression.