Little is known about the prevalence and dynamics of smoking habits among university students in Japan, and their association with other lifestyle parameters and biological markers. Data on undergraduate students were here extracted from the questionnaire and laboratory tests of the periodic health checkup of Kyoto University in 2000 and 2001. In addition to simple statistics, longitudinal analyses were performed using logistic regression, and the odds ratio (OR) and its 95% confidence interval (CI) were calculated for each item. Among 11,203 subjects, 12.1% had a smoking habit. The smoking rate was higher in men than in women (14.4% vs 2.4%, P<0.001) and increased from 2.5% (freshmen) to 18.3% (seniors) with advance in year. During one year of follow-up, 5.8% of students newly acquired a smoking habit, and 12.4% of smokers abandoned the habit. Compared with students majoring in natural sciences, the majors in humanities or social sciences were more likely to begin smoking (OR=1.32, 95% CI=1.06- 1.65). Taking up smoking was more common among those who consumed alcohol (OR=1.98, 95% Cl=1.56-2.51), and skipped breakfast and dined out more frequently (trend P<0.001 for both), but less common among regular exercisers (OR=0.71, 95% Cl=0.56-0.90). Smoking habits tended to be associated with subsequent proteinuria (adjusted OR=1.39, 95% Cl=0.96-2.00) and subsequent cough or phlegm (adjusted OR=1.56, 95% Cl=0.91-2.67). This study revealed that the proportion of student smokers increases with the year in university, in association with several other lifestyle parameters. Measures should be taken against smoking behavior focusing on freshmen and considering their lifestyle.