Inclusion complex formation of hydroxypropyl-gamma-cyclodextrin with benzoic, nicotinic and isomeric aminobenzoic acids in water was studied by calorimetry, H-1 NMR, densimetry and molecular modeling. It was observed that hydroxypropyl-gamma-cyclodextrin selectively interacts with the considered acids forming stable inclusion complexes of 1 : 2 stoichiometry with benzoic and p-aminobenzoic acids, which exist in aqueous solution predominantly as neutral molecules. The binding affinity of hydroxypropyl-gamma-cyclodextrin to m-aminobenzoic and nicotinic acids having the zwitterionic structure is considerably lower and a 1 : 1 inclusion complex is formed only with the former. The binding mode and thermodynamic parameters of complex formation were evaluated. It was shown that they strongly depend on the structure and ionization state of the acids. An efficient molecular modeling approach for simulating the encapsulation process for 1 : 1 and 1 : 2 stoichiometries was developed and implemented. A good agreement between experimental and theoretical results was demonstrated.