Peroxynitrite is a reactive nitrogen species that can mediate protein tyrosine nitration, inactivating many proteins. We show that yeast mitochondrial peroxiredoxin (Prx1p), which belongs to the group 1-Cys-Prx, has thioredoxin-dependent peroxynitrite reductase activity. This activity was characterised in vitro with the recombinant mitochondrial Prx1p, the thioredoxin reductase Trr2p and the thioredoxin Trx3p, using a generator of peroxynitrite (SIN-1). Purified mitochondria from wild-type and null Prx1p or Trx3p yeast strains, exposed to SIN-1, showed a differential inactivation of manganese-containing superoxide dismutase activity. The above yeast strains were exposed to SIN-1 and examined under confocal microscopy. Prx1p or Trx3p-null cells showed a greater accumulation of peroxynitrite than wild-type ones. Our results indicate that this 1-Cys-Prx is a peroxynitrite reductase activity that uses reducing equivalents from NADPH through the mitochondrial thioredoxin system. Therefore, mitochondrial 1-Cys-peroxiredoxin/thioredoxin system constitutes an essential antioxidant defence against oxidative and nitrosative stress in yeast mitochondria.