Gas cluster (GC) ion sources, such as an argon cluster source, have been employed in SIMS of organic or biomaterials due to their low-energy projectile effect. Recently, it was found that GC-SIMS reportedly provides intact ion detection of proteins with molecular weights of 10000 or higher. Since GC-SIMS enables control of the gas cluster size and collision energy per atom, it is considered sensitive for the detection of very small differences in the monolayers of polypeptides such as leu-enkephalin (H-Tyr-Gly-Gly-Phe-Leu-OH) and met-enkephalin (H-Tyr-Gly-Gly-Phe-Met-OH). In this study, both enkephalins were measured with GC-SIMS and their spectra were compared to evaluate GC-SIMS sensitivity to small chemical structure differences. The polypeptides, leu-enkephalin and met-enkephalin, were immobilized on indium-and tin oxide (ITO)-coated glass plates, respectively, by binding their N terminal residues to glutaraldehyde-activated aminosilanized-ITO plates. An aminosilanized-ITO plate without polypeptide was also prepared as the control sample. After freeze-drying, the samples were measured with TOF-SIMS with the argon cluster ion source, and then TOF-SIMS spectra were analyzed to select peaks specific to the polypeptides. As a result, fragment ions related to the polypeptide without recombination were detected using the argon GC-SIMS.