The question of whether cyclodextrin inclusion complexes can be probed with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) was addressed. Such complexes have previously been studied by fast atom bombardment and electrospray ionization, whereas MALDI has rarely been applied. By performing carefully designed control experiments, it was found that cyclodextrin inclusion complexes are destroyed by the MALDI process, either during sample preparation or in the desorption/ionization step. Non-specific electrostatic adducts are formed if an ion-dipole interaction can occur, for example, between the cyclodextrin and a protonated amino group. When investigating pseudorotaxane-like complexes with similar formation constants but with ionic interactions between the complexing partners, it was found that MALDI-MS can detect the specific non-covalent complexes. This work demonstrates that the nature of the interaction in the non-covalent complex is decisive for whether MALDI-MS can probe the specific interaction or not. Finally, it is shown that chemical control experiments are very powerful to complement MS in detecting the presence or absence of a specific non-covalent interaction.