A clinical study on human subjects and using the microcomputed tomography (micro-CT) analysis was conducted to investigate the main morphological and critical parameters of bone and biomaterials structures. Micro-CT was performed in both the phases, preclinical and clinical. In addition, it was combined with histology to analyze the extracted bone four months after implantation. Quantitative analysis of the main morphological parameters as the porosity, the bone volume fraction (BV/TV) and the trabecular thickness (Tb.Th) evidenced the main difference among the biomaterials properties and their influence on the bone tissue regeneration. Qualitative observations by the three-dimensional (3D) reconstruction of the microstructure, contributed to the visualization of the mineralized areas. Micro-CT and its combined application with histology demonstrated as a powerful approach for the microstructural investigation and for the final assessment of the efficacy and effectiveness of the various treatments and implants.