Inclusion, or host-guest, complexes are supramolecular assemblies in which two or more molecules hold together and organize by means of intermolecular noncovalent bonds. In the pharmaceutical field, inclusion complexation of drugs with unsubstituted and derivative β-cyclodextrins (β-CDs) has proven to be a successful method to improve the dissolution of water insoluble drugs. Genistein (Gen), an isoflavone constituent of Onodis spinosae radix, turned out to be a suitable guest molecule for the encapsulation into β-CD, resulting in a significant improvement of its aqueous solubility. In the present study, the modifications of the vibrational spectrum of Gen caused by its inclusion into β-CDs cavity have been characterized by means of Raman scattering experiments. These changes have been interpreted by comparing the experimental data with the vibrational wavenumbers and Raman intensities obtained by simulation for the free and complexed guest molecule. Following this strategy, we have obtained a deeper understanding of the host-guest interactions involved in the formation and stabilization of the complexes, with particular regard to the role played by the guest chemical groups, as well as to disentangle the effects directly related to the complexation process from those ascribed to other factors, such as formation of intra-and intermolecular hydrogen bonds.