Background: This study was undertaken to compare clinicopathologic features and survival between patients with unexpected N1 (clinical N0 - pathologic N1) and expected N1 disease (clinical N1 - pathologic N1) after operation for non-small cell lung cancer. Methods: From 2003 to 2009, 305 patients who were found to have pathologic N1 disease after complete resection were retrospectively analyzed. Among these, 177 patients had negative findings for both computed tomography (CT) and positron emission tomography (PET)/CT (group cN0). Sixty-eight patients had negative CT and positive PET/CT or positive CT and negative PET/CT findings (group cN0-1). Sixty patients had positive findings for both CT and PET/CT (group cN1). Results: Patients in the cN1 group had larger tumors (p < 0.001), greater pathologic T stage (p = 0.018), and greater percentage of squamous cell carcinoma (p < 0.001) than did those in the other groups. Patients in the cN1 group had a greater number of positive N1 lymph nodes (p = 0.004) and more frequent extracapsular nodal invasion (p < 0.001). The 5-year overall survival was 66%, 63%, and 58% in groups cN0, cN0-1, and cN1, respectively (cN0 vs cN0-1, p = 0.958; cN0 vs cN1, p = 0.038). The 5-year disease-free survival was 54%, 52%, and 39% in groups cN0, cN0-1, and cN1, respectively (cN0 vs cN0-1, p = 0.862; cN0 vs cN1, p = 0.01). Conclusions: Patients with unexpected N1 disease showed better survival than did those with expected N1 disease, which seemed to be related to the pathologically minimal extent of the primary tumor and nodal involvement.