The majority of stage I lung cancer patients undergo a complete resection of their tumor; however, they still harbor a considerable risk of mortality due to recurrences. A correlation between the presence of lymph node micrometastases and poor prognosis has been observed. The aim of this study was to correlate the lymph node molecular staging with the 5-year survival and disease-free interval following pulmonary lobectomy for non-small cell lung cancer (NSCLC). A quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) for carcinoembryonic antigen (CEA) mRNA was performed on primary lung tumors and regional lymph nodes from 55 surgically resected NSCLC patients classified as clinical stage I. CEA mRNA was found to be present in all the primary tumors. RT-PCR revealed the presence of cancer cells in the lymph nodes of 20 patients (36.3%) and routine staining detected lymph node metastases in 11 patients. Significant differences in survival and disease-free intervals were observed in patients with lymph node micrometastases versus patients with negative lymph nodes (P=0.0026 and P=0.0044, respectively). Multivariate analyses confirmed that micrometastases were an independent predictor for worse prognosis (P=0.0098) and a short disease-free interval (P=0.0137). This study demonstrated strong correlations between the molecular detection of lymph node micrometastases and 5-year survival rates and disease-free interval in patients who underwent pulmonary lobectomy for early-stage lung cancer.