Energetically highly disfavored geometric isomers are present in only trace amounts in solution and hence cannot be clearly observed by conventional spectroscopic methods. Here, we provide spectroscopic evidence that a suitably sized/shaped cavitand (alpha-cyclodextrin) can discriminate distinctive stereochemical differences between all possible cis-trans stereoisomers of a qualified Compound, showing selective recognition solely for the target unstable isomer. We tested a set of guests, and we were able to obtain, for each one separately, purely thermodynamic selectivity of the host for the energetically highly dispreferred stereoisomer among all other equilibrating geometric isomers under ambient conditions.