The design and synthesis of plasmonic nanoparticles with Raman-active moleculesembedded inside them are of significant interest for sensing and imagingapplications. However, direct synthesis of such nanostructures with controllableshape, size, and plasmonic properties remains extremely challenging. Here wereport on the preparation of uniform Au@Ag core/shell nanorods with controllableAg shells of 1 to 25 nm in thickness. 1,4-Aminothiophenol (4-ATP) molecules,used as the Raman reporters, were located between the Au core and the Ag shell.Successful embedding of reporter molecules inside the core/shell nanoparticleswas confirmed by the absence of selective oxidation of the amino groups, asmeasured by Raman spectroscopy. The dependence of Raman intensity on thelocation of the reporter molecules in the inside and outside of the nanorods wasstudied. The molecules in the interior showed strong and uniform Ramanintensity, at least an order of magnitude higher than that of the molecules on thenanoparticle surface. In contrast to the usual surface-functionalized Raman tags,aggregation and clustering of nanoparticles with embedded molecules decreasedthe surface-enhanced Raman scattering (SERS) signal. The findings from this studyprovide the basis for a novel detection technique of low analyte concentrationutilizing the high SERS response of molecules inside the core/shell metalnanostructures. As an example, we show robust SERS detection of thiramfungicide as low as 10−9 M in solutions.