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The present study investigated expression profiles of the potential CSC markers including CD133, CD44, ALDH1, and β-catenin, and evaluated their prognostic value in lung adenocarcinomas. One-hundred-and-seventy-seven tumors (stage I) were immunohistochemically examined for the expression of these markers, and thresholds to subdivide expression levels were determined using receiver operating characteristics curves. Tumors with high levels of CD133 (adjusted hazard ratio (HR) 4.55 (95% confidence interval (CI) 1.26–16.40,P= 0.021), CD44 (HR 3.73, 95% CI 1.20–11.58,P= 0.023) or ALDH1 (HR 3.61, 95% CI 1.09–12.3,P= 0.036), but not β-catenin (HR 2.43, 95% CI 0.59–10.8,P= 0.220), showed a significantly higher risk of recurrence than the corresponding low expressers. In conclusion, levels of CD133, CD44, and ALDH1 had independent prognostic value to predict the recurrence of lung adenocarcinoma.