Analysis of bone microvascularization has generally been performed from 2D histology. The method proposed in this study enables for the first time to simultaneously analyze, in 3D, the microvascularization and bone microstructure in a rat model. The method is based on the use of quantitative synchrotron micro-computed tomography (SR-μCT) coupled to an automatic image analysis procedure. 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 segmentation of both bone microstructure and microvascularization in cortical and trabecular regions. A large set of 3D quantitative parameters were then extracted from the bone and vascular networks. In particular, we propose a new parameter, utilizing the availability of both microstructures to relate the two, which we dub the vascular-trabecular interdistance (VTI). Due to the short acquisition times of SR-μCT 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 modulated several bone and vessel parameters, including the VTI.