The structural aspects for the complexation of xanthone and fluorenone to alpha- as well as beta-cyclodextrins (CDxs) were explored by combining absorption, fluorescence, and induced circular dichroism studies with theoretical calculations of the optimized structures for the ketone-CDx complexes and their predicted ICD spectra, Detailed information on the similarities and differences for the complexes of these ketones with CDxs was obtained. For both CDxs, the ketones are bound to the rim of the cavity, and deeper penetration is observed for the complexes with beta-CDx. In addition, a 1:2 complex involving alpha-CDx was only observed in the case of fluorenone. Although the two ketones have similar structures, their molecular recognition properties and the resulting structures of the CDx complexes show distinct differences.