The present study aimed to investigate the ability of SS31, a novel mitochondria-targeted peptide to protect against t-BHP-induced mitochondrial dysfunction and apoptosis in 661W cell lines. The 661W cells were treated with various concentrations of SS-31 and an MTT assay was used to determine cell viability. The expression of nitrotyrosine and 8-hydroxydeoxyguanosine (8-OHdG) was detected using immunofluorescent staining. Apoptosis were assessed using Hoechst staining and an annexin V/propidium iodide flow cytometer. Reactive oxygen species (ROS) were detected using MitoSOX (TM) with confocal microscopy. Changes in mitochondrial membrane potential were analyzed using flow cytometry. In addition, the release of cytochrome c was analyzed using confocal microscopy. The viability of the cells improved following treatment with SS31 between 100 nM and 1 mu M, compared with untreated control group. Compared with the t-BHP treatment group (20.0 +/- 3.8%), the number of annexin V-positive cells decreased dose-dependently to 13.6 +/- 2.6, 9.8 +/- 0.5 and 7.4 +/- 2.0% in the SS-31 treated group at concentrations of 10 nM, 100 nM and 1 mu M, respectively. Treatment with SS-31 significantly prevented the t-BHP-induced expression of nitrotyrosine and 8-OHdG, decreased the quantity of mitochondrial ROS, increased mitochondrial potential, and prevented the release of cytochrome c from mitochondria into the cytoplasm. Therefore, the SS31 mitochondria-targeted peptide protected the 661W cells from the sustained oxidative stress induced by t-BHP.