Background: Lung cancer is the leading cause of cancer deaths in the world. Human papillomavirus (HPV) infection and E6 oncoprotein expression are known risk factors for the development of non-small cell lung cancer (NSCLC). This study was performed to evaluate the prevalence of HPV 16/18 E6 oncoprotein expression in patients with NSCLC. Methods: Immunohistochemical stains of the HPV 16/18 E6 oncoprotein were performed in tumor tissues from 68 patients with NSCLC who underwent curative surgery from March 2006 to November 2008. Results: The E6 oncoprotein was expressed in 29.4% of patients with NSCLC and a statistical analysis revealed that E6 oncoprotein expression was significantly higher in females (p=0.028), never smokers (p=0.045), and patients with adenocarcinoma (p=0.022) than that in other patients. Conclusion: The E6 oncoprotein was expressed in 29.4% of patients with NSCLC. Further studies detecting HPV infection and E6 oncoprotein expression in never smoking patients with NSCLC are needed.