NADH dehydrogenase subunit 2, encoded by the mtDNA, has been associated with resistance to autoimmune type I diabetes (T1D) in a case control study. Recently, we confirmed a role for the mouse ortholog of the protective allele (mt-Nd2 a ) in resistance to T1D using genetic analysis of outcrosses between T1D-resistant ALR and T1D-susceptible NOD mice. We sought to determine the mechanism of disease protection by elucidating whether mt-Nd2 a affects basal mitochondrial function or mitochondrial function in the presence of oxidative stress. Two lines of reciprocal conplastic mouse strains were generated: one with ALR nuclear DNA and NOD mtDNA (ALR.mt NOD ) and the reciprocal with NOD nuclear DNA and ALR mtDNA (NOD.mt ALR ). Basal mitochondrial respiration, transmembrane potential, and electron transport system enzymatic activities showed no difference among the strains. However, ALR.mt NOD mitochondria supported by either complex I or complex II substrates produced significantly more reactive oxygen species when compared with both parental strains, NOD.mt ALR or C57BL/6 controls. Nitric oxide inhibited respiration to a similar extent for mitochondria from the five strains due to competitive antagonism with molecular oxygen at complex IV. Superoxide and hydrogen peroxide generated by xanthine oxidase did not significantly decrease complex I function. The protein nitrating agents peroxynitrite or nitrogen dioxide radicals significantly decreased complex I function but with no significant difference among the five strains. In summary, mt-Nd2 a does not confer elevated resistance to oxidative stress; however, it plays a critical role in the control of the mitochondrial reactive oxygen species production.Single nucleotide polymorphisms in the mtDNA have been associated with degenerative diseases and various cancers. Yet sequence changes may also result in resistance to disease.Indeed, a cytosine to adenine transversion (C5178A) resulting in a leucine to methionine substitution in the human NADH dehydrogenase subunit 2 gene (mt-ND2) encoded in the mtDNA has been associated with increased longevity (1, 2) as well as reductions in atherosclerosis (3), blood pressure (4), myocardial infarction (5), and T1D 3 incidence (6). The adenine-containing allele, mt-ND2 a (adenine containing NADH dehydrogenase subunit 2 allele), was also associated with reduced islet autoimmunity as represented by significantly lower titers of autoantibodies against glutamic acid decarboxylase, insulin, and protein-tyrosine phosphatase, receptor type N (Ptprn or IA-2) (6).Insulin synthetic and secretory capacities of pancreatic  cells are highly dependent upon communication between the nucleus and the mitochondria (7) and are reliant upon mitochondrial ATP generation (8). Although mitochondria are critical for the life and function of  cells, there is strong evidence that mitochondria play a central role in apoptotic death of the  cell during autoimmune T1D (9 -16). Therefore, sequence variation in the mtDNA may have profound effects on the  cell...