Despite the excellent performance in clinical practice and research, the dual-energy X-ray absorptiometry is restricted by the inherent planar nature of the measurement and the inability to discriminate between trabecular and cortical components of bone. Recently, a new peripheral tomographic scanner (Norland/Stratec XCT 3000) was introduced for versatile measurements of human long bone characteristics in vivo, including trabecular and cortical density (TrD and CoD, respectively), respective cross-sectional areas (TrA and CoA), bone strength index (BSI), and bone mineral content (BMC). We evaluated the technical performance of the scanner using different phantoms and determined the in vivo precision of the above-noted applications by measuring twice several sites of upper and lower limbs of 19 and 36 volunteers aged 23-60 years. The bone scans were performed, with intermediate positioning of the subject, at two different anatomic sites of the forearm, three sites of the upper arm, three sites of the shank, and two sites of the thigh, with the respective skeletal sites representing different bone compositions and sizes. According to phantom measurements, the XCT 3000 appeared to be a highly linear, stable, and precise (coefficient of variation [CV] about 0.2%) system in vitro. The soft tissue thickness, however, had a linear effect on density values and a nonlinear effect on BMC, whereas the effect on cross-sectional area was marginal. The in vivo root mean square CV (CVrms) values for the long bone ends ranged from 0.9% (distal tibia) to 2.7% (distal femur) for TrD, from 1.8% (distal femur) to 7.6% (distal radius) for TrA, from 2.0% (distal tibia) to 6.8% (proximal tibia) for CoD, from 1.8% (distal femur) to 4.9% (proximal tibia) for CoA, and from 4.2% (distal tibia) to 7.7% (distal radius) for BSI. The corresponding CVrms values for the long bone shafts ranged from 0.5% (midshaft of humerus) to 1.4% (midshaft of fibula) for CoD, from 1.7% (midshaft of tibia) to 4.6% (proximal shaft of humerus) for CoA, and from 2.5% (midshaft of tibia) to 7.5% (proximal shaft of humerus) for BSI. There was no interoperator effect on precision. This study provided, for the first time, independent precision data for the new XCT 3000 peripheral quantitative computed tomography (pQCT) scanner in various applications of human long bones (radius, ulna, humerus, tibia, fibula, and femur) and gave practical guidelines and procedures on how to employ this versatile method in clinical and research applications. The technical performance of the tested system was excellent and it allowed, with a low radiation dose, precise in vivo evaluation of trabecular and cortical density, cross-sectional area, and BMC of selected skeletal sites. The potential effect of the soft tissue thickness on density and mineral content values need to be recognized. The pQCT measurement seems to be useful in supplementing the integral, planar DXA data and obviously opens new possibilities for clinical practice and research.