Prevalent inconsistency of human papillomavirus (HPV) infection in lung cancer was found among recent studies from different countries with racial and geographic variations. Even in Chinese populations, the prevalent discrepancy of HPV infection in lung cancer patients was also found with the geographic variations and tumor types. To study the difference of HPV-16/18 infection in lung squamous cell carcinomas and non-cancer controls, we conducted this study to verify whether there was a similar HPV infection prevalence pattern in lung squamous cell carcinoma patients from the Western part of China. Paraffin-embedded samples (180), of 72 lung squamous cell carcinomas, 37 lung adenocarcinomas and 71 non-cancer controls, were analyzed by INNO-LIPA Genotype polymerase chain reaction (PCR) and real-time PCR analysis. The data showed that 51.4% (37/72) of lung squamous cell carcinoma samples, 16.2% (6/37) of adenocarcinoma, and 22.5% (16/71) of non-cancer controls were HPV DNA positive. The risk of lung squamous cell carcinomas was 3.5 times higher among people HPV-positive (odds ratio 3.5, 95% CI 1.6-7.3, p<0.001) compared with the HPV- negative population. Adjusted by smoking status, the risk of lung squamous cell carcinomas was 3.5 times higher among people HPV-positive (odds ratio 3.5, 95% CI 1.7-7.5, p=0.001) compared with the HPV-negative population. The risk of lung squamous cell carcinomas was 16.9 times higher for patients with positive HPV-16 (odds ratio 16.9, 95% CI 3.8-75.3, p<0.0001) than negative HPV-16. Adjusted by smoking status, the risk of lung squamous cell carcinomas was 17.4 times higher among people HPV-16 positive (odds ratio 17.4, 95% CI 3.9-77.5, p<0.0001) compared with HPV-16 negative people. INNO-LIPA Genotype analysis revealed that the frequency of high risk HPV-16 and 18 genotype in lung squamous cell carcinoma cases appeared to be significant higher than that in the non-cancer controls (P<0.001), and the most frequent genotype was HPV-16 (21 cases), followed by HPV-18 (6 cases), HPV-16/18 (4 cases) in lung squamous cell carcinomas, respectively, and the majority genotype was HPV-6 (9 cases) in controls. The HPV-16 E2/E6 ratio was significantly lower than the unity, suggested that the main presence of integrated form of HPV-16 genome (16/27) may contribute more to lung squamous cell carcinomas, despite its viral load estimated to be only <1 to 2 copies per cell.