Blackbody infrared radiation dissociation is used to probe the fragmentation behavior of peptide-cyclodextrin complexes. Complexes formed by combining bradykinin (and some of its analogues) with permethylated beta-cyclodextrin undergo peptide fragmentation rather than complex dissociation under these conditions. Activation energies and preexponential factors are obtained from Arrhenius plots constructed over a temperature range (between 323 and 440 K). The fragmentation behavior of the peptides does not differ considerably when the sites of inclusions are removed from the peptide. Molecular dynamics simulations are performed to better understand the experimental observations.