The reactions between Pd(II) and low-rim amino acid substituted calix[4]arenes {La = 5,11,17,23-tetra-4-tert-butyl-25,27-di{[(2′-amino-4′-methylthio)-L-butyryl]aminoethoxy}-26,28-dihydroxycalix[4]arene, Lb = 5,11,17,23-tetra-4- tert-butyl-25,27-di({[(N-tert-butoxycarbonyl)-2′-amino-4′-methylthio]-L-butyryl}aminoethoxy)-26,28-dihydroxycalix[4]arene (diN-BOC-La) and Lc = 5,11,17,23-tetra-4-tert-butyl-25,27-di{[(N-tert-butoxycarbonyl)-2′-aminoacetyl]aminoethoxy}-26,28-dihydroxycalix[4]arene} were studied by electrospray mass spectrometry. When La was refluxed with 2.2 equiv. of trans-[Pd(Py)2Cl2] or 1.1 equiv. of PdCl2, the mononuclear complex PdLaCl2 was formed. When refluxed with 2.2 equiv. of PdCl2, the binuclear complex Pd2LaCl4 was obtained. The same binuclear complex Pd2LaCl4 was also obtained as the final adduct when Lb was refluxed with 3.5 equiv. of PdCl2, during which two BOC groups are removed one-by-one after 6 and 16 h, respectively. However, when Lb was refluxed with trans-[Pd(Py)2Cl2] in methanol, no reaction was observed. In order to understand whether the coordination to Pd(II) of the S atom in methionine is necessary for the removal of BOC groups, the reaction of Lc containing diN-BOC-glycine with PdCl2 was also conducted. The result showed that the BOC groups can also be removed and the Pd(II) complex is not formed until both BOC groups are detached from Lc. These data reveal that the detachment of BOC groups is likely induced by PdCl2, which acts as a Lewis acid during the reaction. This method can be potentially applied to the preparation of analogs of Pd(II) and other metal complexes of calixarenes substituted at the lower rim by BOC-protected amino acids or peptides without prior treatment of the BOC groups.