Information is lacking regarding the comparison of bone mineral and body composition measurements obtained from the different dual energy X-ray absorptiometry (DXA) systems. The purpose of this study is to compare body composition and whole body bone mineral density (BMD) measurements from the hologic QDR-4500 W (DXA H) and the lunar (DXA L) systems. Seven women older than 40 years of age, were scanned on the same day by using DXA H and DXA L by the same observer. Measured total fat mass, percentage fat, whole body fat free soft tissue mass and BMD were similar between machines, but body mass was significantly higher with DXA L than with DXA H (P=0.0156). This was due to a higher bone mineral content obtained with DXA L. Agreement between the two DXA systems was quantified by using the Bland and Altman method. For each variable, all pairs of measurements were within the 95% confidence limits. These results suggested that we could use the two measurement methods interchangeably. However, due to the bone mineral inter-machine differences, comparisons of DXA measurements from different machines should be interpreted with caution.