<i>Background:</i> Cytotoxic T lymphocyte antigen 4 (CTLA-4) is a potent immunoregulatory molecule that suppresses antitumor response by downregulating T cell activation. The most studied +49A>G polymorphism of the CTLA-4 gene has been associated with several autoimmune diseases. However, little is known about the association between this functional polymorphism of CTLA-4 and cancer prognosis. <i>Objective:</i> To investigate the association between CTLA-4 +49A>G polymorphism and prognosis of advanced non-small cell lung cancer (NSCLC) patients in a Chinese population. <i>Methods:</i> The CTLA-4 +49A>G polymorphism was detected by polymerase chain reaction-restriction fragment length polymorphism in 338 advanced NSCLC patients. <i>Results:</i> The frequencies of CTLA-4 +49 GG, GA and AA in advanced NSCLC patients were 44.4%, 42.0% and 13.6%, respectively. No significant association was observed between CTLA-4 +49A>G polymorphism and clinicopathologic features of advanced NSCLC including gender, histopathological type, clinical stage and tumor markers. Patients with the AA genotype had a survival time of 9.8 months, significantly shorter than those with the GG genotype (12.5 months) or the GA genotype (12.0 months) (p < 0.001; log-rank test). Multivariate Cox analysis further revealed that the CTLA-4 +49AA genotype is an independent adverse prognostic indicator for NSCLC patients. <i>Conclusion:</i> Our data suggest that the polymorphism of CTLA-4 +49A>G is a prognostic predictor for advanced NSCLC.