To elucidate quantitatively the sidearm effects on the molecular selective binding of aminated beta-cyclodextrins (beta-CD), microcalorimetry titration has been performed in aqueous phosphate buffer solution (pH = 7.20) at 298.15 K to give the complex stability constants (K-s) and the standard free energy (DeltaGdegrees), enthalpy (DeltaHdegrees), and entropy changes (DeltaSdegrees) for the 1:1 inclusion complexation of beta-CD (1), mono(6-amino-6-deoxy)-beta-CD (2), mono(6-carboxymethylamino-6-deoxy)-beta-CD (3), and mono [6-(R(-)-1-hydroxymethylpropylamino)-6-deoxy]-beta-CD (4) with representative bile salts, deoxycholate, cholate, glycocholate, and taurocholate. The results obtained indicate that the aminated beta-CDs could alter significantly the original molecular binding ability and selectivity of parent beta-CD through the cooperative electrostatic interaction, van der Waals, and hydrophobic interactions between hosts and guests. As compared with parent 1 and aminated beta-CD 2, glycine-modified beta-CD 3 possessing a hydrophilic carboxylic group at the sidearm shows a lower binding ability toward bile salts, attributed to the relatively weaker hydrophobic interactions and the electrostatic repulsion between host and guest to some extent. However, the R(-)-2-amino-1-butanol-modified beta-CD 4 possessing additional binding sites at the chiral sidearm could significantly orient the guest molecules to be included in cavity and thus evidently enhances the molecular binding ability and selectivity through steric interactions. Thermodynamically, the higher complex stability for inclusion complexation of aminated beta-CDs is mainly resulting from enthalpy gain with smaller entropy loss. The combination of calorimetric titration experiments and ROESY spectra establishes the correlation between the thermodynamic parameters and the conformation of the resulting complex, and reveals the factors governing the molecular binding ability and selectivity of bile salts by aminated beta-CDs.