Early atherosclerotic change is found even in childhood, and there is an urgent need to clarify the factors causing childhood atherosclerosis and take preventive measures. Early detection of the contributing risk factors is crucial to facilitate preventive measures. Pulse wave velocity (PWV) is a widely used technique for the assessment of atherosclerosis in children.Lifestyle questionnaire, brachio-ankle PWV (baPWV) and anthropometric data were obtained from junior high school students in an urban area of Japan between 2006 and 2008, from seventh to ninth grades.Mean baPWV increased from 867.4 ± 99.5 m/s to 944.5 ± 117.5 m/s in boys, and from 864.0 ± 99.5 m/s to 923.0 ± 101.3 m/s in girls. Obese students had higher baPWV than non-obese students in both genders across each grade. On logistic regression analysis of ninth grade student data, high baPWV was dependent on systolic blood pressure (SBP), time watching television (TV) and symptoms of depression and anxiety, whereas low baPWV was dependent on time playing video games, light exercise, sleep and indoor play, as well as good friendship and motivation.Systolic blood pressure, time watching TV, and symptoms of depression and anxiety may contribute to arterial stiffness and be related to obesity in junior high school students.