Microfocus computed tomography (micro-CT; R_mCT) is a dynamic noninvasive method for measuring bone regeneration. This study evaluated whether R_mCT was equivalent to histomorphometry in assessing bone augmentation. Two plastic caps of graft material with (experiment) or without hydroxyapatite (HA; control) were placed in the exposed calvaria of rats. Images of bone augmentation within the plastic caps were then taken using R_mCT. Histological sections were cut along the same plane as that used for the micro-CT images. Bone regeneration beyond the skeletal envelope occurred at both the experimental and control sites. Bone volume also increased at both sites. In addition, consistent patterns of bone formation were observed in both R_mCT and histological images. R_mCT analysis enables highly quantitative and qualitative measurement of bone augmentation in living animals.