The analysis of intramolecular atomic energies and charges, obtained from QTAIM, strongly and unambiguously suggests that the most stable HL+ form of a linear triamine H2N(CH2)2NH(CH2)3NH2 (L) has the secondary nitrogen atom protonated, contradicting earlier reports. This is supported by the G(aq) value (at the RX3LYP/6-311++G(d,p) level of theory in solvent, CPCM/UAKS) which is lower by about 4 kcal mol–1 (equivalent to three log units of a protonation constant log KH) when compared with remaining HL+ tautomers. The most stable H2L2+ form of L found from QTAIM has two terminal nitrogen atoms protonated, which is in agreement with the existing views. A new rule governing the protonation sequence of linear polyamines is proposed stating that at thermodynamic equilibrium the protonation sequence in a solution results in the formation of tautomers which (i) minimizes the differences in the atomic energies and net atomic charges of both terminal atoms, N and C, in all partially protonated forms, HL+ and H2L2+, and (ii) have a symmetrical distribution of the atomic energies and net atomic charges on the terminal fragments –CH2–NH2 of a linear molecule. Several conditions, involving the atomic energies and charges of the terminal N- and carbon atoms, are defined and incorporated in a protocol which results in a definite prediction of the protonation sequence of linear aliphatic triamines.