Modern diagnostic tools ever aim to reduce the amount of analyte and the time needed for obtaining the result. Surface-enhanced Raman spectroscopy is a method that could satisfy both of these requirements, provided that for each analyte an adequate substrate is found. Here we demonstrate the ability of gold-sputtered silicon nanowires (SiNW) to bind p-mercaptobenzoic acid in 10−3, 10−4 and 10−5M and adenine in 30 and 100μM concentrations. Based on the normal mode analysis, presented here for the first time, the binding of p-mercaptobenzoic acid is deduced. The intensity enhancement of the 1106cm−1 band is explained by involvement of the CS stretching deformation, and the appearance of the broad 300cm−1 band attributed to SAu stretching mode. Adenine SERS spectra demonstrate the existence of the 7H tautomer since the strongest band observed is at 736cm−1. The adenine binding is likely to occur in several ways, because the number of observed bands in the 1200–1600cm−1 interval exceeds the number of observed bands in the normal Raman spectrum of the free molecule. Not annealed (left) Au sputtered Si nanowires are better SERS substrates. Display omitted •Gold-sputtered not annealed silicon nanowire hybrid substrates were prepared by electroless chemical etching.•Not annealed substrates have better surface density of hot spots.•Normal modes of 4-mercaptobenzoic acid were calculated and assigned.