Molecular modeling of flavonoid/β-cyclodextrin complexes was used for rationalization of 1H-NMR data. We describe an algorithm that allows exact definition of the starting host-guest orientation. We used this algorithm to build complexes of two flavonoids, quercetin and myricetin. Subsequent molecular dynamics simulations yielded structures consistent with NMR data for the flavonoid position in the β-cyclodextrin cavity.