Background: Hyperthyroidism is associated with bone mass reduction and increased fracture risk, but the effects on other important bone parameters have been sparsely examined. Therefore, we investigated bone microarchitecture and estimated bone strength by high-resolution peripheral quantitative computed tomography (HR-pQCT) in hyperthyroid patients at diagnosis and after being euthyroid for at least one year. Methods: Two approaches were used: (A) a case-control study comparing 61 hyperthyroid women with 61 euthyroid women matched for age and menopause status; (B) a follow-up study, in which 46 of the 61 women were re-examined after having been euthyroid for one year. HR-pQCT of the distal radius and tibia, and dual-energy X-ray absorptiometry (DXA) of the lumbar spine and the hip were performed. Results: In analysis A: In the radius, compared with the healthy controls, hyperthyroid patients had higher total area (16.9% +/- 29.5%; p < 0.001), trabecular area (28.6% +/- 45.7%; p < 0.001), and lower cortical area (-11.7% +/- 23.2%; p < 0.001). Total volumetric bone mineral density (vBMD) (-13.9% +/- 26.5%; p < 0.001), cortical vBMD (-5.8% +/- 7.9%; p < 0.001), cortical thickness (-16.7% +/- 26.0%; p < 0.001), and estimated bone strength (-6.6% +/- 19.5%; p < 0.01) were lower. No significant differences were found in the tibia or in the DXA parameters. In analysis B: In the radius, significant improvements were observed in the cortical area (2.1% +/- 4.6%; p < 0.01), cortical thickness (2.5% +/- 5.1%; p < 0.001), and total vBMD (0.8% +/- 3.0%; p < 0.05). Trabecular area decreased (-0.5% +/- 1.0%; p < 0.01) and trabecular separation increased (2.0% +/- 8.3%; p < 0.05). In the tibia, cortical area (3.6% +/- 7.3%; p < 0.01) and cortical thickness (3.8% +/- 7.6%; p < 0.01) increased, and trabecular area decreased (-0.5% +/- 1.1%; p < 0.01). Areal BMD, measured by DXA, increased in the spine (1.1% +/- 3.4%; p < 0.05) and in the hip (2.0% +/- 3.8%; p < 0.01). Conclusions: Compared with the healthy control group, hyperthyroid women had lower vBMD, lower estimated bone strength, and compromised cortical microarchitecture in the radius. After restoration of euthyroidism, significant improvements in vBMD and cortical microarchitecture were observed, highlighting the importance of achieving and maintaining euthyroidism.