Abstract <p>Traditional methods for quantitative identification of bacteria require long time, which substantially limits their operational efficiency. This paper proposes a rapid and simple method for counting <i>S. aureus</i> 209p and <i>E. coli</i> K12 bacterial cells on the basis of indirect surface-enhanced Raman scattering (SERS) using gold nanostar and nanorod tags conjugated with 4-nitrothiophenol. An increase in the SERS signal has been shown to depend on the number of nanoparticle-labeled bacterial cells. The developed procedure has appeared to be efficient both for the direct measurement of the signal from the freshly prepared complex and for measuring the signal from the cellular precipitate after centrifugation. The most statistically reliable results have been obtained using gold nanostars under the conditions of the direct precipitate-free measurement of the SERS signal from the bacteria complex.</p>