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The ability of 29 peripheral quantitative computed tomography (pQCT) software analysis modes at defining cortical from trabecular bone at three tibial metaphyseal regions was evaluated using five cadaveric tibiae. The accuracy of pQCT was determined by comparing the bone mineral content (BMC) with the ash weight. The precision of the pQCT scanner was calculated using repeated measurements. All the analysis modes had a good accuracy when measuring total bone area and a poor accuracy when measuring cortical bone area at the proximal 5% and distal 4% regions. For trabecular bone measured at all three regions and cortical bone area measured at the proximal 10% region, the Stratec peel mode 5 was the most accurate analysis mode. Highly significant correlations (r = 0.71–0.98) and a moderate accuracy error (coefficient of variation [CV] = 5–22%) was found between ash weight and BMC when using this mode. The precision of bone mineral density (BMD) measurements was good (total, CV = 2–5%; trabecular, CV = 2–5%; cortical, CV = 4–6%). pQCT is a moderately accurate, precise method of measuring trabecular and total BMD at the tibial metaphysis. The authors recommend caution when interpreting results for cortical BMD, as cortical area measurements at the metaphyseal region are less accurate and less precise.