The importance of the mitochondrion in maintaining normal cellular physiology has long been appreciated. Recently there has been an upsurge in mitochondrial research due to increased recognition that a number of diseases are caused by defective functioning of this key intracellular organelle. Given this, along with advances made in proteomics technologies, the mitochondrion is clearly recognized as a top candidate for proteomics analysis. However, mitochondrial proteomics is not a trivial undertaking due to physicochemical properties that impair the resolution of inner mitochondrial membrane proteins when using conventional proteomic gel electrophoresis procedures. To circumvent such problems, many laboratories have adapted blue native-gel electrophoresis (BN-PAGE), a specialized type of native-gel electrophoresis, to generate high-resolution proteomic maps of the oxidative phosphorylation system. In this short overview the concepts and methods of BN-PAGE are presented, which demonstrate the power of using this complementary proteomics approach to identify alterations in the mitochondrial proteome that contribute to disease.