The ovariectomized (OVX) rat model is well established in investigations of osteoporosis and osteoporotic therapies. Advent of techniques such as Fourier-transform infrared (FTIR) spectroscopy and small angle X-ray scattering (SAXS) facilitate characterization of bone composition and mineral structure, respectively, which are key determinants of bone strength. Limited publications exist on the implementation of these techniques in the OVX rat model. At 12 weeks of age, female Sprague-Dawley rats were either sham-operated (n = 6) or ovariectomized (n = 6) and sacrificed 18 weeks later. L2 lumbar vertebrae and proximal tibiae were assessed by µCT, FTIR and SAXS. Presence of extensive trabecular deterioration in the µCT data confirmed the onset of osteoporosis. FTIR compositional parameters were determined including measures of degree of mineralization, crystallinity, collagen maturity and acid phosphate content. Mineral crystal thickness was determined from the SAXS data using two approaches available in literature. Compositionally, a decline in the heterogeneity of acid phosphate content was observed while measures of crystallinity and collagen maturity remained unaltered. Using an iterative curve fitting method, OVX-induced increases in the mineral crystal thickness of 3.8 and 7.8 % (p < 0.05) were noted in the trabecular of the vertebra and tibia, respectively. In conclusion, implementation of FTIR and SAXS techniques in the OVX rat model, identified no significant compositional changes while substantiating thickening of the mineral crystals as a general structural feature of OVX-induced osteoporosis in rats.