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Oxidative stress, especially peroxynitrite (ONOO(-))-mediated oxidative stress, plays a key role in diabetes. Mitochondria, as the generating source of ONOO(-), may also be the major damaging target of ONOO(-), which can cause a series of mitochondrial proteins nitration. Therefore, this study aimed to clarify the relationship between the nitration of entire mitochondrial proteins induced by ONOO(-) and liver mitochondrial structural damage in diabetes. Sprague-Dawley male rats were injected with streptozotocin to induce diabetes. After 10 weeks, transmission electron microscopy was used to observe the ultrastructure of liver mitochondria, and reverse transcription-polymerase chain reaction was used to detect liver inducible nitric oxide synthase (iNOS) mRNA expression. Nitrotyrosine (NT) content and distribution were detected with Western blot analysis and immunohistochemistry. In addition, some biochemical indicators were detected to represent oxidative stress and metabolic disorders. In diabetic rats, increasing levels of iNOS mRNA and NT content (P.05) were observed, in accord with pathological alterations of the ultrastructure of liver mitochondria. Meanwhile, some alterations in biochemical indicators were observed in diabetes. Treatment with aminoguanidine could significantly attenuate these alterations (P.01 or P.05). In conclusion, the nitration of mitochondrial proteins induced by ONOO(-) may be responsible for structural damage to liver mitochondria, and aminoguanidine can reduce ONOO(-) generation and attenuate mitochondrial damage.