Background Few studies have reported on the effects of the energy expenditure estimated from the frequency of exercise on bone mass, bone metabolic marker and bone related hormones in young females. The goal of this study is to examine the indices related to bone metabolism such as the bone metabolism markers and hormones and clarify their association with the bone mass through their relationship to exercises. Methods A total of 190 premenopausal Japanese females aged 20-49 years participated in this study. The calcaneus stiffness index (SI) was measured by ultrasound bone densitometry. The subjects' past and present exercise was measured using the self-administered questionnaire. Urinary deoxypyridinoline (DPD), 1,25-dihydroxyvitamin D3, intact parathyroid hormone (PTH), and bone specific alkaline phosphatase (BAP) were determined. Results DPD was shown to be a strong negative predictor of the SI (p<0.05). Energy expenditure by exercise only during senior high school in the exercise history was shown to be a positive predictor of the SI (p<0.05). Energy expenditure by exercise only during senior high school was shown to be a significant negative predictor of the DPD (p<0.05). Conclusion It has been revealed that the amount of energy expenditure from physical activity during the subject's high school years affects the levels of SI and DPD in adulthood.