Direct characterization of peptides with multiple disulfide bonds by mass spectrometry is highly desirable. In this study, electron transfer dissociation (ETD) of peptide disulfide regio-isomers was studied using model peptides containing two intrachain disulfide bonds. ETD provided rich sequence information (c/z ions) even for the backbone region under the coverage of two disulfide bonds. This behavior presented an analytical advantage over low energy collision-induced dissociation (CID) of protonated intact peptide ions, which produced very limited sequence (b/y) ions. Mechanistic studies suggested that the formation of c/z ions under the two disulfide bond covered region resulted from an initial N–C_α bond cleavage, followed by radical cascades to cleave multiple disulfide bonds. The ETD spectra of the disulfide regio-isomers produced similar product ions due to radical cascades; while the relative intensities of the product ions varied, to a certain degree, which could be helpful in distinguishing isomers with overlapping disulfide bonds.