Background The purpose of the present study was to assess the value of matrix metalloproteinase (MMP)-2 and MMP-9 expression and other potential prognostic factors in predicting the clinical outcome of patients after definitive surgery for pathologic stage IA non-small cell lung cancer (NSCLC). Methods One hundred and forty-six consecutive and non-selected patients who underwent definitive surgery for stage IA NSCLC were included in this study. Formalin-fixed paraffin-embedded specimens were stained for MMP-2 and MMP-9, which were statistically evaluated for their prognostic value and other clinicopathological parameters. Results Of the 146 patients studied, 102 (69.9%) cases were classified as having high expression for MMP-2. A total of 89 carcinomas (61.0%) had high expression for MMP-9. MMP-9 expression correlated with Eastern Cooperative Oncology Group (ECOG) performance status, pT stage, and differentiation (P = 0.005, <0.001, and <0.001, respectively). Vessel invasion, pT stage, and MMP-9 expression maintained their independent prognostic influence on overall survival (P = 0.037, <0.001, and <0.001, respectively). Conclusions From results of our relatively large database, MMP-9 may be considered as a viable biomarker that can be used in conjunction with other prognostic factors such as vessel invasion and pT stage to predict the prognosis of patients with completely resected pathologic stage IA NSCLC. J. Surg. Oncol. 2011; 104:841-846. © 2011 Wiley Periodicals, Inc.