We have established a technique for quantification of collagen and bone minerals using synchrotron radiation (SR) CT and second harmonic generation (SHG) microscopy. This technique was used to evaluate the anabolic effect of whole body micro-vibration (WBMV) on bone defect healing. Male C57BL/6JJcl mice aged 13 weeks were operated to drill a 0.5-mm hole in the right tibial diaphysis. Two days after the drill-hole injury, the animals were randomly assigned to a WBMV (n=6) or a control (n=6) grou The WBMV group was exposed to a sine wave vibration (0.03g, 30Hz) and the control group to sham treatment for 20 min/day over 10 days. Bone specimens were then harvested and images of the bone mineral density and collagen density (SHG signal intensity) in the defect were acquired by SRCT and SHG microscopy, respectively. After image registration by maximizing mutual information from SRCT and SHG data, we quantified the bone mineral and collagen densities in the regions where bone and collagen overlapped in the defect. Mineralization was promoted in WBMV but collagen density did not differ between two groups. No correlation was found between the SHG signal intensity and the mineral density in both groups. These results suggest that WBMV probably promotes repair of bone defect by enhancing mineral deposition while having no influence on collagen density.