A new type of encoded bead, which uses surface-enhanced Raman scattering (SERS), is described for multiplex immunoassays. Silver nanoparticles were embedded in sulfonated polystyrene (PS) beads via a polyol method, and they were used as SERS-active substrates. Raman-label organic compounds such as 4-methylbenzenethiol (4-MT), 2-naphthalenethiol (2-NT), and benzenethiol (BT) were then adsorbed onto the silver nanoparticles in the sulfonated PS bead. Although only three kinds of encoding have been demonstrated here, various combinations of these Raman-label organic compounds have the potential to give a large number of tags. The Raman-label-incorporated particles were then coated with a silica shell using tetraethoxyorthosilicate (TEOS) for chemical stability and biocompatibility. The resulting beads showed unique and intense Raman signals for the labeled organic compounds. We demonstrated that SERS-encoded beads could be used for multiplex detection with a model using streptavidin and p53. In our system, the binding event of target molecules and the type of ligand can be simultaneously recognized by Raman spectroscopy using a single laser-line excitation (514.5 nm).