Osteoporosis is a metabolic bone disease characterized by reduced bone mass and deterioration of bone microarchitecture. It results from the shift of the osteoblast–osteoclast activity equilibrium in favor of the later. Although, a number of biochemical markers, such as collagen I N-telopeptide (NTx) and osteocalcin (OC), have been used for monitoring bone remodeling, a new, monitoring, non-invasive method, which is based on the measurement of the dynamic characteristic of bone and is known as modal damping factor (MDF), has not been evaluated as a diagnostic tool for osteoporosis. Bisphosphonates, such as alendronate, have an established role in the treatment of osteoporosis. The aim of the present study was, therefore, to evaluate the effects of alendronate on the levels of MDF, serum NTx and OC on osteoporosis induced by ovariectomy in rats. Furthermore, the effects of alendronate on osteoporosis have been histologically evaluated. Fifteen adult female Wistar rats were bilaterally ovariectomized and osteoporosis was histologically confirmed and by the use of peripheral quantitative computerized tomography (pQCT). MDF was applied to assess the bone structural integrity.