Inclusion complex formation of hydroxypropylated α-, β- and γ-cyclodextrins with riboflavin (vitamin B2) and alloxazine was studied by spectroscopic and solubility methods. Alloxazine, which is a structural analog of riboflavin, was considered in order to evaluate the role of ribityl and methyl substituents in complexation. Thermodynamic parameters for 1:1 complex formation were obtained and analyzed in terms of influence of the reagent structure on the binding process. It was shown that the cavity of hydroxypropyl-β-cyclodextrin is more appropriate for formation of stable complexes. The complexes are enthalpy stabilized, due to prevalence of van der Waals interactions and possible hydrogen bonding. The partial insertion of riboflavin into the cyclodextrin cavity was revealed by 1H NMR and computer modeling. The ribityl side chain, which prevents deep inclusion, is located nearby the wider rim of the cyclodextrin molecule and can undergo destruction. Penetration of the alloxazine molecule into the macrocyclic cavity is deeper and accompanied by formation of more stable inclusion complexes. Hydroxypropyl-β-cyclodextrin was found to be the more efficient solubilizing agent for riboflavin and alloxazine, whereas a stabilization action of cyclodextrins towards riboflavin was not observed.