Protonation pathways of 2-amino-4-benzylsulfanyl-6-methylpyrimidines have been investigated by means of semiempirical PM3 quantum-chemical simulation, ¹³ C NMR spectroscopy, and single-crystal diffractometry methods. In the gas phase and in the bipolar aprotic solvent, the protonation involves the N ¹ atom. The protonation in the crystalline state is characterized by the formation of a branched system of H-bonds, involving the protons of the amino group besides the mentioned nitrogen atom.