Mitochondria are the major intracellular sites of oxygen consumption producing reactive oxygen species (ROS) as toxic by-products of oxidative phosphorylation, primarily via electron leakage from the respiratory chain. The resultant types of chemical damage to lipids, DNA and proteins are described as well as the broader implications for the involvement of ROS in disease onset and progression. The relative contributions of mitochondrial, enzyme-linked, antioxidant defence systems to tissue protection are also reviewed as is the emerging importance of the peroxiredoxin family in general to H2O2-mediated signalling The constituent enzymes of the mitochondrial PrxIII pathway are discussed in detail including the roles of PrxIII and PrxV in their capacities as typical 2-cys and atypical 2-cys thioredoxin-dependent hydroperoxide reductases, respectively. The structures and catalytic mechanisms of PrxIII and V are examined and some key properties of the reconstituted mitochondrial PrxIII pathway are highlighted with specific reference to the susceptibility of peroxiredoxins to inactivation at elevated H2O2 levels and their potential for participation in H2O2-mediated signalling responses. It is concluded that mitochondrial Prxs form a vital link in an integrated cellular antioxidant defence network that minimises ROS-mediated damage and ensures that cells mount appropriate responses to increased levels of oxidative stress via the upregulation of key cell signalling pathways.