The goal of this study was to evaluate the expression of MUC1 in stage IB non-small cell lung cancer (NSCLC) and its prognostic significance. The expression of MUC1 in 178 NSCLC specimens was evaluated via immunohistochemistry. A reproducible semiquantitative method which took both staining percentage and intensity into account was applied for immunohistochemical scoring, and receiver operating characteristic curve analysis was utilized to select the cut-off score for high or low MUC1 expression. Then, the correlations between MUC1 expression and clinicopathological features and its prognostic relevance were determined. In this study, high MUC1 expression was detected more frequently in adenocarcinomas (86.3%) and other NSCLCs (74.1%) than in squamous cell carcinomas (39.1%, P < 0.001). The Kaplan-Meier survival curves showed that up-regulated expression of MUC1 indicated poorer overall survival (OS) and disease-free survival (DFS) (P = 0.011 and P = 0.008, respectively), especially for those with non-squamous cell carcinomas (P = 0.033 and P = 0.011, respectively). Multivariate analysis also confirmed that MUC1 expression was an independent prognostic factor for both OS and DFS in stage IB NSCLC (P = 0.008 and P = 0.004, respectively). MUC1 might be correlated with the histogenesis of lung adenocarcinoma, and its elevated expression may be an adverse prognostic indicator for the patients with stages IB NSCLC, particularly for those with non-squamous cell carcinomas.