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A reduced bone perfusion has been found for osteoporotic subjects in previous studies. However, the physiological changes underlying the varied perfusion function is not well known yet. Tofts model is one of the most frequently used pharmacokinetic models in analyzing perfusion process. This study modified the Tofts model by replacing the arterial input function (AIF) by a new algorithm. The modified model was then employed to analyze vertebral bone marrow perfusion in subjects with different bone mineral density (BMD). Eighty-two male subjects were involved in this study and classified into three groups (normal, osteopenia, and osteoporosis) according to T-score. BMD was measured by dual-energy X-ray absorptiometry (DXA). The quantitative parameters derived from the pharmacokinetic model, Ktrans (extravasation transfer efficiency for blood perfusion) and ve (extravascular extracellular space for blood perfusion), showed a significant reduction in subjects with lower BMD, respectively. The results suggested that with the bone mineral content lost, the vascular wall properties as well as the bone marrow content may also vary. The resultant perfusion change may also influence the bone nutrition supply in reverse.