Smoking is a risk factor for oral leukoplakia and oral cancer, as well as lung cancer, cardiovascular diseases and many other systemic diseases. Smoking is considered increasing factor of some oral diseases involved indigenous bacteria. In addition, a relationship between smoking and infection of Human papillomavirus (HPV), which is associated with oropharyngeal cancer, remains unclear. The aim of this study is to assess whether smoking has an impact on increase of bacteria inducing oral disease such as dental caries and periodontitis, and HPV infection. DNA of saliva gathered from smokers and non-smokers, consisted of men and women, was analyzed using PCR. Oral disease-causing bacteria were more detected in men smokers than men non-smokers and HPV was most found in women non-smokers. Taken together, this study suggests smoking is related with variation of oral microorganism existence in some way.