A subgroup analysis on the basis of the expression of CSC markers indicated that although Bmi-1 (HR = 1.97, 95% CI 1.35–2.87, P < 0.001), CD44s (HR = 2.59, 95% CI 1.32–5.06, P = 0.005; I2 = 61.63%, Ph = 0.1), and CD44V6 (HR = 3.29, 95% CI 1.46–7.43, P = 0.004; I2 = 61.63%, Ph = 0.1) are significantly associated with GC patients CSS/DSS, CD44V9 (HR = 1.67, 95% CI 0.52–5.35, P = 0.38; I2 = 0.00%, Ph = 0.48) and LGR-5 (HR = 1.02, 95% CI 0.67–1.54, P = 0.9) are not associated. Here, BMI1 is linked to gastric cancer.