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A new method for simultaneous 3D imaging and analysis of microvascularization and bone microstructure in rat bone is developed. The method is based on the use of quantitative synchrotron micro-computed tomography (SR-muCT) coupled to an automatic image analysis procedure. Analysis of bone microvascularization is generally performed from 2D histology. The proposed method enables for the first time the simultaneous 3D analysis of microvascularization and bone microstructure in a rat model. It was applied to investigate the effect of intermittent parathyroid hormone (PTH) administration on angiogenesis and osteogenesis in rats. Rats were posthumously injected with a contrast agent and subsequently imaged. The algorithm allowed the reconstruction and the extraction of 3D quantitative parameters both on bone microstructure and microvascularization. Due to the short acquisition times of SR-muCT and the efficiency of the image analysis algorithm, a large data set was analyzed, which permitted statistical analysis of the measured parameters. Statistical analysis confirmed that treatment with PTH significantly increased bone volume and thickness, but decreased bone mineralization. It was further revealed that treatment with PTH significantly increased average vessel thickness.