The adsorption structure of uracil on gold and silver nanoparticle surfaces has been comparatively studied by means of surface-enhanced Raman scattering (SERS). Uracil appeared to assume a perpendicular orientation with respect to the surfaces. The presence of the nu(CH) band in the SERS spectra indicated a vertical orientation of the aromatic ring of uracil on Au and Ag. The density functional theory (DFT) calculation was performed at the levels of B3LYP and MP2 to estimate the energetic stability of the N3- and N1-deprotonated tautomers and their vibrational frequencies on the surfaces. Almost all the vibrational bands in the SERS spectra at high concentrations could be ascribed to the N3-deprotonated uracil. The N3-deprotonated tautomer was predicted to be more favorable on Au than on Ag from the DFT calculation. The metal-N bond distance was assumed to be shorter for Au than for Ag upon adsorption of uracil.