High-resolution peripheral quantitative computed tomography (HR-pQCT) was upgraded to a second generation in 2014 with higher spatial resolution, faster scan time, and a different measurement algorithm. The purpose of this study was to investigate the precision of the second-generation HR-pQCT. The distal radius and tibia of 15 healthy men and women (age range of 20–74 yr, 8 men and 7 women) were scanned by second-generation HR-pQCT, and their geometry, bone mineral density (BMD), and the microstructure of trabecular and cortical bones were evaluated. Scans and measurements were performed by tester 1 at baseline and at 1 and 4 wk to evaluate intratester reproducibility, and by testers 2 and 3 one time each to evaluate intertester reproducibility. Reproducibility was evaluated by root mean square percent coefficient of variance (RMS%CV). Factors involved in the reproducibility of cortical porosity (Ct.Po) were also investigated. The ranges of RMS%CV were 0.2%–2.5% for geometry, 0.6%–1.7% for BMD, 0.7%–2.4% for trabecular bone, and 1.1%–1.3% for cortical thickness, showing excellent reproducibility. The range of RMS%CV for Ct.Po was 11.0%–13.3%, relatively higher than those for the other parameters. There was no apparent difference between intra- and intertester reproducibilities. There was no clear correlation between the percent coefficient of variance of Ct.Po and the subjects' background characteristics, motion artifact, and cortical bone structure. The reproducibility of the second-generation HR-pQCT was excellent in geometry, BMD, trabecular bone, and cortical thickness, with no apparent difference between intra- and intertester reproducibilities. Compared with the first-generation HR-pQCT, the reproducibility of trabecular bone was improved. The reproducibility of Ct.Po was insufficient and needed to be improved, and factors that influence its reproducibility were not clear.