Our previous reports have indicated that high risk human papillomarvirus (HPV) 16/18 were much more frequently detected in lung tumors of female patients as compared to that of male patients and HPV 16/18 in lung tumors were evolutionally correlated with those in blood circulation. In the other hand, it is well known that HPV 6/11 are frequently associated with upper aerodigestive and respiratory diseases. HPV 6/11 DNA were detected in lung tumors by nested PCR and in situ hybridization to investigate if any difference in prevalent types of HPV exists between genders. Our data showed that HPV 6 infection was detected in 28.4% (40 of 141) lung tumors, which was significantly higher than that in non-cancer controls (1.7%, 1 of 60; P < 0.0001), however, such high prevalence was not observed for HPV 11. Among studied clinico-pathological parameters, HPV 6 infection was significantly related with gender (P = 0.002) and smoking status (P = 0.014). After being stratified by gender and smoking status, HPV 6 infection rate in lung tumors of non-smoking male patients was much higher than that in non-smoking female patients (33.3% versus 11.1%; P = 0.023), but no difference between smoking and non-smoking male patients (38.1% versus 33.3%). With adjustments for age, tumor type, and tumor stage, smoking male lung cancer patients had a much higher OR value (OR, 7.35; 95%CI, 2.11-25.58) for HPV 6 infection compared with 3.93 (95% CI, 1.17-13.12) of non-smoking male patients. Moreover, a higher prevalence of HPV 6 was detected in lung tumors of smoking male patients with early tumor stage than those with advanced stages (P = 0.008), but not in non-smoking male and female patients. A higher prevalence of HPV 6 in male lung cancer patients, as compared with female lung cancer patients, indicating not only different HPV infection routes for different genders, but also that HPV 6 infections may act as a prospective early risk marker of lung cancer for smoking male patients in Taiwan.