The applicability of the electronegativity equalization method (EEM) is investigated for the calculation of atoms-in-molecules charges in prototypical organic molecules. A large training set of molecules was composed, comprising H, C, N, O, and F. Geometries and atomic charges are calculated at the B3LYP/6-31G* level, and from the calculated charges, effective electronegativity and hardness values are calibrated in a least-squares fashion. The quality of the EEM charges is assessed by comparison with B3LYP/6-31G* charges calculated for a test set of amino acids and the neuroleptic fluanisone, not contained in the training set. The EEM approach is found to be a very powerful way to obtain AIM charges without the computational cost of the ab initio approach.