The aim of this chapter is to review the application of vibrational spectroscopy and microspectroscopy, namely FTIR and Raman spectroscopy and microspectroscopy in the diagnosis of drug- or disease-induced bone and cartilage disorders. The first section gives an introduction on the structure and composition as well as diseases of bone and cartilage and summarizes diagnostic techniques used to quantify and qualify these changes. This section also mentions the advantages and disadvantages of currently used diagnostic techniques and vibrational spectroscopy and microspectroscopy. The second and third sections describe protocols for tissue preparation, data processing and analysis for FTIR and Raman spectroscopy and microspectroscopy. The last section presents the application of these vibrational techniques for detailed molecular investigation of the disorders in bone and cartilage. Specific examples are provided to illustrate the application of cluster analysis, analysis of secondary structure, etc.