Technical Abstract: A piglet model was used to determine the variations in measurements from different software algorithms used in the same type of dual energy X ray absorptiometry (DXA) instruments from the same manufacturer. Forty-one piglets (6190 +/- 5856g, mean +/- SD) were scanned in duplicate with a fan-beam densitometer (Hologic QDR4500A, Hologic Inc, Bedford, MA) in the infant whole body scan mode. The same scans were analyzed with two software versions: vKH6 (validated with carcass chemical measurement) and v11.2 (commercial software from the same densitometer manufacturer). All analysis values were highly correlated (r = 0.90 to 1.00) and DXA values for total weights were almost identical. However, v11.2 results consistently overestimated bone mineral content (49.3 +/- 23.4%, mean +/- SD), bone area (21.1 +/- 8.2%), bone mineral density (24.1 +/- 22.2%), and fat mass (160.9 +/- 71.7%) but underestimated lean mass (-14.3 +/- 5.5%) when compared to the values from vKH6. Differences between software versions increased with heavier piglets. The commercial software for fan-beam DXA measurement of piglets, matched for the size of human infants and young children, has major inaccuracies for bone mineral and body composition that become further exaggerated with increasing weight of the subject.