Although mitochondrial reduction-oxidation (redox) stress and increase in membrane permeability play an important role in diabetic-associated renal microvasculopathies, it is unclear whether the intra-renal mitochondrial oxidative stress induces mitochondrial protein modifications, leading to increase mitochondrial membrane permeability. The hypothesis is that mitochondrial oxidative stress induces mitochondrial protein modification and leakage in the mitochondrial membrane in type-2 diabetes. The present study was conducted to determine the involvement of intra-renal mitochondrial oxidative stress in mitochondrial protein modifications and modulation of membrane permeability in the setting of type-2 diabetes. Diabetes was induced by 6-week regimen of a high calorie and fat diet in C57BL/6J mice (Am J Physiol 291:F694-F701, 2006). Subcellular fractionation was carried out in kidney tissue from wild type and diabetic mice. All fractions were highly enriched in their corresponding marker enzyme. Subcellular protein modifications were determined by Western blot and 2-D proteomics. The results suggest that diabetes-induced oxidative stress parallels an increase in NADPH oxidase-4 (NOX-4) and decrease in superoxide dismutase-1, 2 (SOD-1, 2) expression, in mitochondrial compartment. We observed loss of mitochondrial membrane permeability as evidenced by leakage of mitochondrial cytochrome c and prohibitin to the cytosol. However, there was no loss in control tissue. The 2-D Western blots for mitochondrial post-translational modification showed an increase in nitrotyrosine generation in diabetes. We conclude that diabetes-induced intra-renal mitochondrial oxidative stress is reflected by an increase in mitochondrial membrane permeability and protein modifications by nitrotyrosine generation.