Functional inactivation of RUNX3 through epigenetic silencing was well-documented in many cancers. Added to gene mutation and promoter hypermethylation, cytoplasmic mislocalization was another major manifestation of RUNX3 dysfunction in malignancies like gastric cancer. We aimed to investigate whether NSCLC patients with different RUNX3 expression patterns would have differrent OS, and the associations of different patterns with clinicopathologic parameters and clinical outcome. Expressions of RUNX3 and Ki-67 were immunohistochemically detected in normal lung tissue (n=5) and surgically resected NSCLC patients (n=188). The optimal cutoff of RUNX3 was determined by X-tile software related to their survival. Apoptotic index in cancerous tissue was evaluated by TdT mediated dUTP-biotin nick end labelling (TUNEL) method. The prognostic significance of different expression patterns of RUNX3 was determined by means of Kaplan-Meier survival estimates and log-rank tests. Loss of RUNX3 expression in NSCLC was correlated with low cancerous apoptotic index (P<0.001), shorter OS and worse prognosis (P=0.0142), while no statistical difference of apoptotic index (P=0.73) or survival (P=0.3781) had been determined between patient subgroups with different localization of RUNX3 expression. Loss of expression rather than cytoplasmic mislocalization of RUNX3 predicted worse outcome in NSCLC, which was quite different from what it manifested in other cancer types.