QTAIM atomic and bond properties as well as delocalization indices computed on B3LYP/6-311++(2d, 2p) and MP2/6-31++G(d, p) electron densities are employed to explain the protonation preference of indole for C3 site. In spite of displaying a very small increase of its total electron population, N1 is significantly stabilized in the preferred protonation due to an important loss of pi electron population slightly exceeded by an increase of sigma one. C2 and C8 are the atoms that reflect the largest changes of electron population in all C-protonations. 6-centre delocalization indices indicate that the preferred protonation increases the aromaticity of the benzenoid ring. (c) 2006 Elsevier B.V. All rights reserved.