Label-free surface-enhanced Raman spectroscopy (SERS) detection of nucleic acid hybridization is impeded by poor spectral reproducibility and the fact that the chemical signatures of hybridized and unhybridized sequences are highly similar. To overcome these issues, highly reproducible silver nanorod SERS substrates along with a straightforward least-squares (LS) technique have been employed for the quantitative determination of the relative ratios of the four nucleotide components A, C, G, and T/U before and after hybridization using a clinically relevant micro-RNA sequence.