1H NMR spectroscopy was applied to study the catalytic activity of dinuclear Pd(II)-aqua complexes with different benzodiazine bridging ligands, [{Pd(en)(H2O)}2(μ-qx)]4+ (Pd1), [{Pd(en)(H2O)}2(μ-qz)]4+ (Pd2) and [{Pd(en)(H2O)}2(μ-phtz)]4+ (Pd3) (qx, qz and phtz denote quinoxaline, quinazoline and phthalazine, respectively), in the hydrolytic cleavage of the amide bond in N-acetylated L-methionylglycine (Ac–L–Met–Gly) and L-histidylglycine (Ac–L–His–Gly) dipeptides. All reactions were investigated with an equimolar amount of the reactants at pH = 2.0–2.5 in D2O and at 37 °C. The obtained data for the catalytic activity of Pd1–Pd3 complexes are compared with those previously reported for [{Pt(en)(H2O)}2(μ-L)]4+ (L denotes benzodiazine: qx, qz and phtz), [{Pd(en)(H2O)}2(μ-L)]4+ and [{Pt(en)(H2O)}2(μ-L)]4+ (L denotes diazine: pyrazine and pyridazine) complexes. It was found that catalytic activity of these complexes in peptide cleavage is strongly related to the position of the nitrogen atoms in the benzodiazine or diazine bridging ligand. The investigated dinuclear Pd(II) and Pt(II) complexes show catalytic activity in the selective hydrolysis of the Met–Gly amide bond of Ac–L–Met–Gly dipeptide. Moreover, all the above mentioned Pd(II) complexes were also able to catalyze the regioselective hydrolysis of the His–Gly amide bond of Ac–L–His–Gly dipeptide. However, in the reaction with Ac–L–His–Gly, only Pt(II) aqua complexes containing bridging ligands with two nitrogen atoms in the para-position (quinoxaline and pyrazine) were able to cleave this dipeptide.