Subgroup analysis indicted that high expression of CD133 (HR = 2.33, 95%CI: 1.42–3.83, P < 0.001), Oct-4(HR = 2.10, 95%CI: 1.36–3.22, P = 0.007) and Nanog (HR = 2.49, 95%CI: 1.66–3.72, P < 0.001) could predict poor OS in HNSCC patients respectively whereas overexpression of Bmi-1 was not related to the reduced OS in HNSCC patients (HR = 1.32, 95%CI: 0.66–2.65, P = 0.43). The gene discussed is NANOG; the disease is head and neck squamous cell carcinoma.