In a typical bone tissue engineering application, osteogenic cells are harvested and seeded on a three-dimensional (3D) synthetic scaffold that acts as guide and stimulus for tissue growth, creating a tissue engineering construct or living biocomposite. Despite the large number of performed experiments in different laboratories, information on the kinetics of bone growth into the scaffolds is still scarce. Highly porous hydroxyapatite scaffolds were investigated before the implantation and after they were seeded with in vitro expanded bone marrow stromal cells (BMSC) and implanted for 8, 16, or 24 weeks in immunodeficient mice. Synchrotron x-ray computed microtomography (microCT) was used for qualitative and quantitative 3D characterization of the scaffold material and 3D evaluation of tissue engineered bone growth kinetics after in vivo implantation. Experiments were performed taking advantage of a dedicated set up at the European Synchrotron Radiation Facility (ESRF, Grenoble, France), which allowed quantitative imaging at a spatial resolution of about 5 microm. A peculiarity of these experiments was the fact that at first the data were obtained on the different pure scaffolds, then the same scaffolds were seeded by BMSC, implanted, and brought again to ESRF for investigating the formation of new bone. The volume fraction, average thickness, and distribution of the newly formed bone were evaluated as a function of the implantation time. New bone thickness increased from week 8 to week 16, but deposition of new bone was arrested from week 16 to week 24. Instead, mineralization of the newly deposited bone matrix continued up to week 24.