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The newest version of whole body dual-energy X-ray absorptiometry (DXA) analysis software from Hologic (Discovery 12.1) is designed to enhance bone detection in smaller subjects. We re-analyzed 1127 pediatric scans (ages 1.8–18.5 yr) previously analyzed using software version 11.2. Regression analysis compared new and original results for bone area (BA), bone mineral content (BMC), bone mineral density (BMD), and DXA-derived body weight. Changes in total and regional bone results were compared with age, weight, and height. New results were highly correlated with original analyses (R2 > 0.9), but there were large differences at the individual subject level. The BA and BMC values increased in subjects less than 40 kg weight, resulting in a lower BMD. Original and new results were equivalent by about age 14 yr in both genders. Regional bone data showed the greatest changes in the legs. The newest software produces significant changes in bone values in subjects weighing less than 40 kg, compared with earlier versions. This effect increases with decreasing body weight. This will impact interpretation of longitudinal pediatric DXA studies, as well as existing pediatric whole body bone reference databases. Investigators must recognize which DXAsoftware version they are using, and which version produced any reference database they may use for comparison.