Non-covalent complexation of mono- and bisphosphonates by hexaglucosylthioureidocalixarene and octaglucosylthioureidocalix[ 8]arene was studied by electrospray ionisation Fourier transform ion cyclotron resonance mass spectrometry. Glucosylthioureidocalixarene formed 1:1 and 1:2 complexes with bisphosphonates, with a marked preference towards risedronate, clodronate, zoledronate and etidronate. In contrast, up to four guest molecules were bound in the case of monophosphonates, suggesting a different type of binding in comparison to bisphosphonates. Hexaglucosylthioureidocalix[ 6]arene also formed complexes with phosphonates with a somewhat similar binding selectivity. Interestingly, the addition of calcium ions into the sample of etidronate–glucosylthioureidocalixarene complex resulted in a complete release of the guest due to the very high affinity between calcium and bisphosphonate. In the gas-phase hydrogen/deuterium exchange reactions, glucosylthioureidocalixarene exhibited a number of exchangeable hydrogens and a bimodal exchange distribution was observed, suggesting a presence of multiple gas-phase conformations. Surprisingly, no exchange or very slow exchange for the complexes of glucosylthioureidocalixarene was observed.