Complex formation between quinine and natural cyclodextrins (CD) was studied using NMR spectroscopy. The strongest association was observed for complexes of neutral quinine molecule with βCD. Association constants for monokationic quinine were one order of magnitude smaller, while dikationic quinine did not bind to CDs. Distribution of complexation-induced shifts and ROESY spectra revealed bimodal quinine binding in complexes built up by βCD and γCD. Complex formation resulted in decrease of vicinal coupling constant between H2 and H9 protons owing to the rotation about C2–C9 bond and in consequence in mutual reorientation of two main constituents of quinine: quinoline and quinuclidine. DFT calculations allowed to establish that H2 and H9 protons are antiperiplanar in the prevailing quinine conformer(s) in aqueous solution. Conformers with synclinal H2, H9 protons become to participate in quinine complexed with CDs.