OBJECTIVE The purpose of this study is to investigate factors influencing the osteo-sono assessment index (OSI) in junior high school students (boys, girls who had reached menarche, and girls who had not). METHODS A total of 9,743 students (4,974 boys and 4,769 girls) in Ehime Prefecture participated in this study. We measured body mass index (BMI) and calcaneal bone mass using OSI. In parallel, participants answered a questionnaire relating to age, sex, menarche, exercise habits, milk intake, and history of bone fractures during the preceding year. To determine the factors influencing OSI, we calculated an individual standardized partial regression coefficient (β) using multiple linear regression (MLR) analysis. RESULTS For boys, MLR showed that BMI (β = 0.300), age (β = 0.260), current exercise habits (β = 0.106), and milk intake per day in primary school (β = 0.085) statistically significantly influenced OSI. For girls who had reached menarche, BMI (β = 0.302), current exercise habits (β = 0.237), age (β = 0.140), and bone fracture during the preceding year (β = 0.036) influenced OSI. For girls who had not reached menarche, current exercise habits (β = 0.242), BMI (β = 0.135), and age (β = 0.085) influenced OSI. CONCLUSIONS There were differences between the factors related to OSI among boys, girls who had reached menarche, and girls who had not. BMI, exercise habits, and age were the common factors related to OSI. Particularly for girls, exercise habits had a great influence on OSI.