Nitric oxide (NO) regulates several cellular functions via reversible regulation of mitochondrial respiration. Nitric oxide also reacts with mitochondrial superoxide anion to produce the potent oxidative species peroxynitrite that irreversibly hinders mitochondrial activities. Recent findings demonstrating that mitochondria produce NO via mitochondrial NO synthase (mtNOS) has intrigued several laboratories revealing crucial roles for mtNOS-derived NO and peroxynitrite in regulating the functions of mitochondria, cells and organs. The present article reviews the current understanding of the interactions between mitochondria, and NO and peroxynitrite.