We compared bone mineral density (BMD) and body fat percentage (%fat) between two pencil-beam (Lunar DPX and DPX-L) and two fan-beam (Lunar Prodigy, Hologic Delphi A) dual-energy X-ray absorptiometry (DXA) systems. We examined these values in the total-body, spine, femur, and forearm scans in 78 healthy adults across these four DXA systems. BMD and %fat values were highly correlated among the four instruments. DPX-L gave the lowest mean %fat and Prodigy gave the highest mean %fat for both sexes. The means were system dependent for %fat estimates across the four DXA machines. There was a significant difference detected in BMD estimates across manufacturers, with the Delphi A providing systematically lower values than the Lunar systems in the whole body, spine, and femur sites but higher values than the Lunar systems in the forearm. The present study results show that both %fat and bone mineral estimates between pencil-beam and fan-beam systems are highly correlated, but vary by system. Significant differences exist between the instruments, especially between different manufacturers, and most of the comparisons are sex dependent. We conclude that longitudinal studies should always be evaluated on the same system when possible, and translation models should be used to assess cross-instrument differences.