Purpose: To determine the optimal dilation pixel size distance from the mini-implant interface needed to compensate for the metal artifact on micro-computed tomography (micro-CT) for bone morphometric analysis. Materials and Methods: A total of 72 self-drilling mini-implants were placed into the buccal alveolar bone of six male beagle dogs. After 12 weeks of orthodontic loading, specimens were harvested and scanned with micro-CT (Skyscan 1076) at a resolution of 9 µm. Using the reload plug-in and dilation procedure of CTAn, the percentage of bone-implant contact (BIC) and bone volume density (BV/TV, bone volume/total volume), respectively, were measured from one to seven pixels from the metal implant surface. Each pixel size of dilation (PSD) were compared with that of a ground histologic section, and the optimal PSD for bone morphometric analysis using micro-CT was determined. Results: BIC values from micro-CT analysis decreased when the PSD increased (P .05). BIC from micro-CT showed the highest correlation coefficient with BIC from histologic slides when the PSD was 5 to 7 (P .05), whereas BV/TV from micro-CT showed a very high correlation with BV/TV from histologic slides in all ranges (P .0001). Conclusion: To measure BIC and BV/TV using micro-CT, at least 5 PSD from the metal implant surface is needed.