It has become increasingly clear that infrared micro-spectroscopy (IRMS) can be an extremely valuable analysis tool when determining the chemical composition of biological and biomedical samples. Frequently, fluorescence illumination is required for sample characterization, which previously required the use of a separate optical microscope. We report the development and use of a single microscope for both fluorescence microscopy and synchrotron IRMS. This unique combination has been used to identify changes in the composition of newly remodeled bone after the onset of osteoporosis. In addition, other ongoing biomedical applications are discussed.