After introducing the basics and the most relevant experimental aspects of surface-enhanced Raman scattering (SERS), nanostructured metal substrates used as substrates in this technique are discussed. First, general characteristics are considered, and then colloidal and noncolloidal substrates are specifically addressed. Both bottom-up and top-down strategies for substrates preparation are discussed, along with commonly used characterization techniques. A third part is specifically dedicated to how SERS substrates can be used for in vitro and in vivo diagnostics and theranostics, stressing the two different “direct” and “indirect” detection strategies, and the role of the nanobio interface.