While it is well known that hyperthyroidism is associated with decreased bone mineral density, other Dual Energy X-ray Absorptiometry (DXA) derived indices, such as proximal hip geometry and body composition parameters, have not been well studied in India. This study was undertaken to comprehensively assess DXA-derived parameters and bone turnover markers in premenopausal women aged 25-45 years, and to compare these with age- and BMI-matched female controls. This was a case-control study done over a period of one year. Premenopausal women aged 25-45 years with a diagnosis of Graves’ disease were recruited from the Endocrinology outpatient department (OPD) and healthy controls from the community by sample-level matching. Evaluation of bone biochemistry and assessment of DXA-derived indices were carried out. Forty-one premenopausal subjects with hyperthyroidism and 73 age- and BMI- matched controls were recruited into the study. The mean BMD at lumbar spine(LS), femoral neck(FN) and trabecular bone score were significantly lower among cases as compared to controls, while bone turnover markers were higher in subjects with hyperthyroidism (p < 0.05). Measures of proximal hip geometry were impaired in Graves' disease as compared to controls, with significant differences being noted in CSA at NN [2.57 ± 0.34 vs 2.83 ± 0.50 cm; P = 0.015], SM/Z at NN [1.09 ± 0.20 vs 1.22 ± 0.21 cm; P = 0.008] and CSA at IT [4.56 ± 0.82 vs 5.06 ± 1.11 cm; P = 0.037]. A significantly greater proportion of cases had sarcopenia when compared to controls (27% versus 1.4%; p < 0.001). In rural premenopausal subjects from southern India with hyperthyroidism, a comprehensive assessment of bone health demonstrated significant differences in proximal hip geometry, trabecular microarchitecture and body composition as compared to healthy controls.