Many proteins contain free thiols that can be modified by the reversible formation of mixed disulfides with low-molecular-weight thiols through a process called S-thiolation. As the majority of these modifications result from the interaction of protein thiols with the endogenous glutathione pool, protein glutathionylation is the predominant alteration. Protein glutathionylation is of significance both for defense against oxidative damage and in redox signaling. As mitochondria are at the heart of both oxidative damage and redox signaling within the cell, the glutathionylation of mitochondrial proteins is of particular importance. Here we review the mechanisms and physiological significance of the glutathionylation of mitochondrial thiol proteins.