The importance of mitochondrial dysfunction in numerous diseases has long been appreciated. The impact of oxidative and nitrosative stress on mitochondrial function is complex; however, recent progress in the field using proteomics technologies has begun to shed light on the molecular defects responsible for mitochondrial and cellular dysfunction. This review focuses on the state-of-the-art technologies being used and current research endeavors in the field of mitochondrial proteomics with emphasis on those advancements being made in the field of free radical biology to identify the importance of alterations to the mitochondrial proteome in the development of disease.