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Background: Osteoporosis in women is a serious health problem. The relationships between biochemical markers of bone turnover and bone mineral density (BMD) in women have been reported, but no study has examined relationships between tartrate-resistant acid phosphatase-5b (TRACP-5b) or bone-specific alkaline phosphatase (BAP) and bone mass measured by quantitative ultrasound (QUS) in Japanese post-menopausal women. Aim: To investigate the serum TRACP-5b and BAP levels and to determine their associations with the heel stiffness index measured by QUS in post-menopausal women. Subjects and methods: The subjects were 510 post-menopausal women who were invited to participate in periodic health examinations in 2011-2013 (the Unzen Study). The heel stiffness index (bone mass) was measured by QUS. Serum samples were collected and TRACP-5b and BAP levels were measured. Results: Multiple regression analysis showed that a higher log (TRACP-5b) was correlated with a lower stiffness index ( p  = 0.014) and log (BAP) was not correlated with stiffness index after adjusting for covariates ( p  = 0.136). Conclusion: Higher rates of bone resorption are associated with a lower stiffness index in Japanese post-menopausal women. These results may indicate that high bone resorption affects bone mass more than bone formation, resulting in a low bone mass.