Purpose: The aim of this study was to develop a protocol to analyze the microstructure of mandibular and maxillary bone in association with implant placement in ectodermal dysplasia (ED) and anodontia conditions compared to patients not suffering from such conditions. Materials and Methods: This study was not additionally invasive, since the bone harvesting was completed at the time and site of implant placement. Bone samples were allocated into two groups (ED and control patients) and specified by the site of bone harvesting. Microcomputed tomography (micro-CT) analysis at 5-µm resolution was conducted on each bone sample. Computer analysis applying specialized CT analysis and software allowed evaluation of the three-dimensional microstructure of alveolar and basal bone samples for comparison of structural parameters. Results: Ten bone samples (five alveolar and five basal) were harvested. Preliminary data confirmed the structural features and significant differences between alveolar and basal bone. Basal bone had greater absolute and percent bone volume, greater bone surface, and a lower trabecular bone pattern factor than alveolar bone. Conclusion: Preliminary data were derived from bone harvested from both the maxilla and mandible of control patients, while bone samples from ED patients were harvested from only the anterior mandible. Further bone samples will provide more data on whether broader areas of bone harvesting, age, or sex affect the quality and quantity of the bone and influence implant treatment outcomes.