The surface properties of substrates made of 3 nm gold nanoparticles embedded on SiO2 nanospheres enabled fingerprint detection of thiabendazole (TBZ), crystal violet (CV) and 4-Aminothiophenol (4-ATP) at an ultralow concentration of similar to 10(18) M by surface enhanced Raman spectroscopy (SERS). Gold nanoparticles of an average size of similar to 3 nm were synthesized and simultaneously embedded on SiO2 nano spheres by the electron irradiation method. The substrates made from the 3 nm gold nanoparticles embedded on SiO2 nanospheres were successfully used for recording fingerprint SERS spectra of TBZ, CV and 4-ATP over a wide range of concentrations from 10(6) M to 10(18) M using 785 nm laser. The unique features of these substrates are roughness near the surface due to the inherent structural defects of 3 nm gold nanoparticles, nanogaps of <= 1 nm between the embedded nanoparticles and their high number. These produced an abundance of nanocavities which act as active centers of hot-spots and provided a high electric field at the reporter molecules and thus an enhancement factor required to record the SERS spectra at ultra low concentration of 10(18) M. The SERS spectra recorded by the substrates of 4 nm and 6 nm gold nanoparticles are discussed. (C) 2018 Published by Elsevier B.V.