The geometries of various tautomers and rotamers of moxonidine in both anionic and protonated forms were optimized using the two-layered ONIOM(B3LYP 6-311+G(d,p): AM1) method. The calculations showed that, in agreement with experiments, moxonidine exists in a more stable imino tautomer. The tautomer containing,the amino group is less stable by about 19 kJ/mol. The computed stable conformation for the moxonidine species is characterized by the pyrimidine and imidazolidine rings being in the mutual gauche conformation to one another. In contrast to the parent neutral molecule of moxonidine, ionization caused considerable geometric changes in the anions compared to the neutral species. In the neutral form and anion of the parent drug, an intramolecular hydrogen bond stabilizes the structure and makes the most stable conformations more planar. The primary protonation site is the imidazolidine part of drug. The proton affinity of moxonidine was computed to be 1004 kJ/mol. The moxonidine base was found to be less lipophilic than the base of parent clonidine.