Disulfide bonds are critical structural elements in proteins and stabilize folded structures. Modification of these linkages is associated with a loss of structure and function. Previous studies have reported large variations in the rate of disulfide oxidation by hypohalous acids, due to stabilization of reaction intermediates. In this study we hypothesized that considerable variation (and hence selective oxidation) would occur with singlet oxygen (¹O₂), a key intermediate in photo-oxidation reactions. The kinetics of disulfide-mediated ¹O₂ removal were monitored using the time-resolved 1270 nm phosphorescence of ¹O₂. Stern-Volmer plots of these data showed a large variation (∼10³) in the quenching rate constants k_q (from 2 × 10⁷ for α-lipoic acid to 3.6 × 10⁴ M⁻¹s⁻¹ for cystamine). The time course of disulfide loss and product formation (determined by LC-MS) support a role for ¹O₂, with mono- and di-oxygenated products detected. Elevated levels of these latter species were generated in D₂O- compared to H₂O buffers, which is consistent with solvent effects on the ¹O₂ lifetime. These data are interpreted in terms of the intermediacy of a zwitterion [–S⁺(OO⁻)–S–], which either isomerizes to a thiosulfonate [–S(O)₂–S–] or reacts with another parent molecule to give two thiosulfinates [–S(O)–S-]. The variation in quenching rates and product formation are ascribed to zwitterion stabilization by neighboring, or remote, lone pairs of electrons. These data suggest that some disulfides, including some present within or attached to proteins (e.g., α-lipoic acid), may be selectively modified, and undergo subsequent cleavage, with adverse effects on protein structure and function.