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Non-small-cell lung cancer (NSCLC) is a common fatal malignancy worldwide and has a high mortality rate and poor prognosis.The aim was to study the potential prognostic role of markers of cancer stem cells in NSCLC.The associations between the expression of CD44, CD133, and E-cadherin and the clinicopathological variables were evaluated in 65 cases of NSCLC, including 33 adenocarcinoma (ADC), 27 squamous cell carcinoma (SCC), and five cases of large-cell carcinoma using immunohistochemical method.CD44 was expressed in all cases of ADC and SCC. In ADC, it was significantly related to low tumor grade and absence of lymphovascular invasion (LVI) (P>0.001, both), whereas in SCC, it was significantly correlated with low grade (P>0.001). CD133 expression was detected in 39.4% of ADC cases and in 40.7% of SCC cases. CD133 expression was significantly associated with low grade and absence of LVI (P = 0.048 and 0.017, respectively). Normal E-cadherin was seen in only 47.7% of cases of NSCLC. In ADC cases, a significant relationship has been observed between abnormal E-cadherin expression and high grade (P=0.005), LVI (P=0.003), lymph node metastasis (P>0.001), and low CD44 expression (P=0.002), whereas in SCC, a significant relationship has been found between abnormal E-cadherin and both grade of differentiation (P=0.028) and low CD44 expression (P=0.02).CD44 and CD133 are associated with favorable clinicopathological prognostic factors, whereas E-cadherin expression correlates with high-grade tumor, LVI, lymph node metastasis, and low CD44 expression.