The structural aspects for the complexation of (+)-catechin (CA) and (-)-epicatechin (EC) (an enantiomer) to beta-cyclodextrins (CDs) were explored by using a semi-empirical PM3 method. In the beta-CD/CA inclusion complex, the orientation in which the aromatic A-ring of CA projects onto the 2-OH/3-OH face of beta-CD, and the B-ring projects from the 6-OH face is preferred in the binding energy (BE). In contrast, the inclusion of the B-ring of EC from either the secondary hydroxyl group side or the primary hydroxyl group side gives rise to the two most probable complexes. The molecular modeling results are in agreement with the NMR observations and molecular dynamics (MD) simulations. EC forms a more stable complex with beta-CD than the corresponding CA, as judged from the difference in BE. The differential interactions between each enantiomer and the chiral host give rise to the significant structural differences for the corresponding inclusion complexes. Numerous host-guest C-Hcdots, three dots, centeredO interactions, resulting from induced fit of the hosts toward each of the enantiomeric guests, comprise a third significant component besides the O-Hcdots, three dots, centeredO hydrogen bonds and the van der Waals contacts.