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Rearrangement of disulfide bonds during the synthesis of α‐conotoxin GI using PhS(O)Ph/CH₃SiCl₃ oxidation procedure was observed. We have demonstrated that the protecting scheme (order of acetamidomethyl (Acm) and ^tBu protecting groups) of the Cys residues as well as the reaction time influenced the ratio of the native and the mispaired compounds, while the temperature of the reaction mixture had no significant effect. However, in all cases the nonnative derivative was produced in high amount. The structure of the isomers was identified by the combination of enzymatic digestion and mass spectrometry measurements. We conclude that the air oxidation followed by the application of Tl(tfa)₃ for the regioselective formation of disulfide bonds leads up to the appropriate compound in the case of the synthesis of α‐conotoxin GI, while the oxidation procedure using PhS(O)Ph/CH₃SiCl₃ system resulted in the …