Novel Raman tags called nanoaggregate-embedded beads (NAEBs) have been developed. NAEBs are silica-coated, dye-induced aggregates of a small number of metal nanoparticles. In this work, the Raman reporters used to induce aggregation of gold nanoparticles include strongly binding dyes such as XRITC, TRITC, and DTDC and weakly binding dyes such as R6G. Surface enhanced Raman scattering (SERS) signal from a single NAEB can be detected. This study also demonstrates that these SERS-active beads can be used as Raman tags for bio-detection.