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Patients with non-small cell lung cancer (NSCLC) and incomplete resection have poor clinical outcomes. The present study aimed to identify risk factors for disease progression and mortality. A total of 65 patients with early-stage NSCLC that underwent operation but had a non-R0 resection between August 2011 and December 2020 were included in the present study, and the clinicopathological features and driver gene mutation status were analyzed. The median follow-up time was 36.2 months; 39 patients (60.0%) experienced disease progression and 3 patients (4.6%) died. In total, 22 patients (33.8%) harbored mutations in driver genes. Multivariate analysis demonstrated that the presence of driver gene mutations was associated with an increased risk of disease progression [adjusted odds ratio, 24.08; 95% confidence interval (CI), 2.77–209.01; P=0.004]. Tumors classed as Eastern Cooperative Oncology Group performance status 2 [adjusted hazard ratio (HR), 3.49; 95% CI, 1.10–11.03; P=0.033], stage II–IIIB tumors (adjusted HR, 2.55; 95% CI, 1.06–6.17; P=0.037) and the presence of a driver gene mutation (adjusted HR, 3.28; 95% CI, 1.55–6.94; P=0.002) were associated with a significantly reduced progression-free survival (PFS). Driver gene-targeted therapy was associated with an increased post-progression survival for patients that were reported to have disease progression (adjusted HR, 0.38; 95% CI, 0.16–0.91; P=0.030). There was no significant impact of driver gene mutation status on the overall survival (OS) of patients. Although the presence of a driver gene mutation was associated with an increased risk of disease progression and a reduced PFS, it was demonstrated that patients with disease progression may benefit from driver gene-targeted therapy, as patients with driver gene-targeted therapy had a similar OS compared with that of patients with a driver gene-negative or unknown status. Therefore, early comprehensive analysis of driver gene mutation status may be recommended for early-stage NSCLC cancer patients experiencing non-R0 resection. [ABSTRACT FROM AUTHOR]