Surface-enhanced Raman spectroscopy (SERS) holds promise for rapid, in situ detection of perchlorate (ClO4-) in the environment if sensitive and reproducible SERS substrates can be developed. In this study, new, functionalized gold-silica (Au-SiO2) composite nanoparticles were synthesized and used as SERS substrates for ClO4- detection. These nanoparticles were composed of a silica core with Au nanoparticles grafted onto the SiO2 spheres by in situ chemical reduction of AuCl4- or physisorption of Au colloids. Chemical coupling agents with such functional groups as -N+(CH3)3 and -NH3+/-NH2 were used to enhance perchlorate sorption onto the substrate and therefore the detection of ClO4-. These new substrates were found to be optically stable and provide a greatly enhanced surface plasmon or SERS, resulting in a detection limit as low as 10(-6) M ClO4- (0.1 mg/L) in water.