Biocompatible, photostable, and multiplexing-compatible surface-enhanced Raman spectroscopic tagging materials have been developed that are composed of gold nanorod (GNR)-embedded silica particles and organic Raman labels. GNR-embedded silica particles were prepared with different surface coverage by the assembly of GNRs on silica particles based on an electrostatic interaction and subsequent coating of silica with controllable thickness. This method allows the incorporation of various organic Raman labels to generate intense surface-enhanced Raman scattering (SERS) spectra. Furthermore, SERS-active particles are demonstrated as novel Raman tags for immunoassay. The results suggest SERS tags can be used for multiplex and ultrasensitive detection of biomolecules.