Fluoride stimulates bone formation, whereas bisphosphonates reduce bone resorption. In clinical trials, both treatments increase bone density, although sodium fluoride (NaF) increases and alendronate (biphosphonate, ALN) decreases bone turnover. In a comparative study using minipigs an inverse correlation has been reported between bone turnover and elastic modulus. Small-angle X-ray scattering (SAXS) measurements of these bones revealed no structural deterioration of the collagen/mineral composite at the nanometer range for ALN-treated vertebra, whereas a slight increase of the average thickness of the mineral crystals as well as changes of the structure of the collagen/mineral composite were found in the bones of NaF-treated animals. In this study we used quantitative backscattered electron imaging (qBSE) to investigate the cancellous bones from ribs of minipigs treated with vehicle, NaF, or ALN. This method provides information on the local mineral concentration in the micrometer range. Mineralization spectra were obtained from each treatment group, and statistically significant differences between ALN and controls were found for the peak position, the peak height, the peak width, and the average calcium (Ca) concentration of the mineral distribution. The results reveal that the cancellous bone matrix was more uniformly mineralized after ALN treatment. The reduced bone turnover induced by ALN, documented histomorphometrically could be at the origin of this phenomenon. No significant differences were detected between NaF and control. Together with the earlier SAXS data these results may explain in part the increase in bone density and the improvement of biomechanical properties observed after ALN treatment in animals and in osteoporotic patients.