Fourier Transform Infrared microspectroscopy (FTIRM) is as a method to measure bone quality at the microscopic level and is becoming a powerful tool in helping to better understand changes in fragile bone. FTIRM focuses an infrared beam through a tissue section causing molecular bond vibrations which produces absorption peaks at specific wavelengths. These absorption peaks provide information on bone composition such as mineral:matrix ratio, carbonate substitution within the hydroxyapatite matrix, collagen maturity and collagen fibre bond alignment. It has proven to be a useful method in detecting changes in bone quality between normal and osteoporotic bone, particularly when bone mineral density measurements and biochemical markers fail to distinguish fracture patients from nonfractured patients. This method has predominantly been used in the field of bone biology to analyse bone composition in thin sections from mice, but is also applicable to larger cortical samples by reflectance-based FTIRM, which allows thicker tissue sections from rabbit and monkey bones to be analysed. Our unique approach in studying bone composition has been to use synchrotron-based FTIRM in combination with fluorescent labels to account for heterogeneous tissue age where bone surfaces may be undergoing formation and/or resorption. This allows for the analysis of bone composition as a function of anatomic location and bone maturity. This has provided new insights into not only the quality of bone, but also the process by which it mineralises. More recently, we have applied this method to evaluating how current and emerging therapeutics modify bone composition at different bone surfaces.