Secondary ion mass spectrometry (SIMS) is a versatile analytical technique that uses an energetic beam of ions to eject atoms and molecules from a sample surface. The ability to finely focus the impinging ion beam allows chemical maps of a sample surface to be produced while the gradual erosion of a sample under an ion beam bombardment provides access to a third dimension of chemical information. Both hard and soft materials are accessible for analysis by SIMS with the caveat that the technique operates at high vacuum and hence samples may need to be prepared or preserved (e.g., cryogenically) for optimum results. This chapter provides an overview of the fundamentals of the technique, recent progress in instrument development including the introduction of gas cluster ion beams (GCIBs) for SIMS analysis and the resulting development of new mass analyzer configurations to maximize the potential of these beams for mass spectrometry. and examples of applications in bioengineering and biomaterial analysis highlighting pre-clinical application, cancer research and neuroscience applications along with biomaterial development.