Dual energy x-ray absorptiometry (DEXA) measures bone mineral content (BMC), bone mineral density (BMD), fat-free mass (FFM), and provides estimates of percent body fat. Changes in scan mode geometry (pencil beam vs array) may impact these measures and body composition estimates using multi-compartment models. Forty-one adults, ages 59-79 yr, were scanned in each mode and also underwent hydrostatic weighing and measurement of total body water (tritiated water dilution). The effect of scan mode on measurement of DEXA BMC, BMD, FFM, and percent body fat (DEXA %Fat) was examined. The effect of scan mode on percentage body fat determined by a 4-compartment body composition model (4 Comp %Fat) and comparison of DEXA %Fat and 4 Comp %Fat were also examined. BMC and DEXA %Fat were greater (1.3% and 3.9%, respectively, P < 0.01), and BMD and FFM were lower (1.1% and 1.9%, respectively, P < 0.01) with the array scan mode. The 4 Comp %Fat was significantly greater (0.2%) when the array scan mode measurements of total body bone mineral were used; however, these differences were physiologically inconsequential. Comparison between DEXA %Fat and 4 Comp %Fat measures revealed a total error of +/-5.0% in the older adults examined. These results indicate significant scan mode differences in total body BMC, BMD, FFM, and DEXA %Fat measurements and demonstrate the importance of using a single DEXA scan mode for clinical investigation, particularly with longitudinal studies. For all investigations with DEXA, the scan mode should be reported. Furthermore, the error associated with using DEXA alone to estimate percent fat in an older population suggests that this technique is unacceptable in a research setting.