Sugammadex, a new modified gamma cyclodextrin, reverses the neuromuscular blockage induced by rocuronium by forming a strong complex with this muscle relaxant. To evaluate possible interactions with potentially co-administered drugs, interactions between sugammadex and penicillins were investigated using the affinity capillary electrophoresis method for the first time. Capillary electrophoresis coupled to an ultra violet detector was used as an analytical device for the analysis and detection of cyclodextrin inclusion complexes. Changes in the effective mobility of guest drugs (amoxicillin, ampicillin, oxacillin, dicloxacillin and azlocillin) were correlated with the increasing concentration of host molecules in background electrolyte, and successfully fitted into a non-linear curve equation; assuming 1:1 stoichiometric interaction. The calculated association constants (Ka) were: 383.44, 184.54, 265.34 and 95.06 M−1 for amoxicillin, ampicillin, oxacillin and dicloxacillin, respectively. No complex formation with sugammadex could be detected for both penicillin G and piperacillin. The difference in the chemical structure of the penicillins, especially in the (R) side chains, is suggested to be responsible for the variety of binding strength between penicillins and sugammadex. The displacement study demonstrated that interactions between sugammadex and co-administered penicillins could reduce the pharmacological effects of both.