Apolipoprotein(apo)A-I(Milano) (R173C) and apoA-I(Paris) (R151C) are rare cysteine variants of wild-type (WT) apoA-I that possess novel antioxidant properties on phospholipid surfaces. Yet, the two variants differ in their ability to inhibit lipid peroxidation. In this study, we used synthetic peptides (18mers) to investigate the structural basis for the difference in antioxidant activity between apoA-I(Milano) and apoA-I(Paris). A peptide (aa 167-R173C-184) based on the amphipathic alpha helix harboring the R173C mutation inhibited superoxide anion-mediated oxidation of phospholipid in a dose-dependent manner, but it failed to directly quench superoxide anions in aqueous solution, indicating that the peptide acted at the level of phospholipid to inhibit lipid peroxidation just like the full-length cysteine variant. Peptide 145-R151C-162 based on the helical segment containing R151C exhibited the same capacity as peptide 167-R173C-184 to inhibit lipid peroxidation. Thus, the difference in antioxidant activity between apoA-I(Milano) and apoA-I(Paris) was not governed by the primary amino acid sequence of their individual amphipathic alpha helices, rather contextual constraints within the full-length variants set the difference in antioxidant activity. Cysteine-free peptides were weak inhibitors of lipid peroxidation. These results suggest that thiol-bearing helical peptides based on apoA-I(Milano) may be useful to combat inflammatory related diseases.