The objective of the study was to assess the agreement of the Lunar Prodigy with the newer Lunar iDXA dual-energy X-ray absorptiometer for determining total body and regional (arms, legs, trunk) bone mineral density (BMD), bone mineral content (BMC), fat mass (FM), lean tissue mass (LTM), total body mass, and percent fat. Ninety-two healthy adult males (n = 36) and females (n = 56) were scanned consecutively on the iDXA and the Prodigy dual-energy X-ray absorptiometers. For iDXA, relative to Prodigy, paired t tests indicated significantly lower estimates for total body and regional BMD and BMC (p < 0.001). Measures of total body and trunk FM, LTM, and percent fat did not differ between the instruments. In regional analyses, estimates of FM and percent fat were greater, and that of LTM was lower, in the arms (p < 0.001). In contrast, iDXA estimates of LTM were higher in the legs (p < 0.001). All body composition measures were significantly correlated (p < 0.001). Bland-Altman analyses indicated that significant bias existed between iDXA and Prodigy for total body and regional BMD estimates (p < 0.001) such that iDXA underestimated BMD to a greater extent in persons with higher values. In addition, iDXA overestimation bias existed for FM in total body, arms, and legs, and the overestimation was primarily observed in participants with greater body fat (p < 0.001). When combining or comparing data from iDXA with those from Prodigy, investigators should be aware that certain total body and regional estimates are significantly different. The greatest percent differences were observed for arm BMD, FM, and percent fat.