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To evaluate bone mineral density considering its distribution, fractional quantitative computed tomography (fQCT) was designed and verified.Quantitative computed tomography (QCT) was performed at 64 areas in 10 swine long bones. Fractional quantitative computed tomography was measured at the identical areas as the proportion of pixels showing a bone density higher than 130 mg/mL equivalent. All target areas were extracted and incinerated to measure apparent ash bone density. Based on standard references, the accuracy and precision of fQCT were evaluated and the results were compared with conventional QCT results.The correlation coefficient between fQCT and apparent ash bone density was 0.843 (P < 0.0001). The fQCT showed good correlation with volume fraction (r = 0.88, P < 0.0001). The coefficient of variation of fQCT was 0.42%. The fQCT revealed higher accuracy and precision than the results of QCT.Fractional quantitative computed tomography was designed and verified as a reliable method to measure bone mineral density.