Emergence of two near-infrared windows for in vivo and intraoperative SERS

•The first NIR clear window (650–950nm) is far superior for in vivo and intraoperative optical imaging than visible light.•The second NIR clear window (1000–1700nm) can further improve detection sensitivity, spatial resolution, and tissue penetration.•Surface-enhanced Raman scattering (SERS) allows in vivo and intraoperative spectroscopy both in the first and second NIR windows.•The major advantages of SERS nanoparticle tags include photostability, detection sensitivity, and spectral multiplexing.•Further studies are still needed to understand the in vivo fate and long-term safety/toxicity of encoded SERS nanoparticles.