Two-dimensional 1H—15N NMR HSQC/HMBC experiments enable the unambiguous determination of the protonation (methylation) position and tautomeric structure of nitrogen-containing heterocycles. In investigated thiopyrimidines protonation (or methylation) occurs at the N(1) atom of the pyrimidine ring. The tautomeric structures of these compounds were established based on the analysis of 1H—15N NMR spectra. Ab initio calculations of chemical shifts (GIAO B3LYP/6-31G(d)//HF/6-31G) are in full agreement with experimental values. The stability of various protonated (methylated) and tautomeric species is explained in terms of a thermodynamic approach.