The present review article takes into consideration the most important aspects of lipid peroxidation in mitochondria. Firstly the various ways by which lipid peroxidation is induced and the relevant mechanisms are described and discussed. After examining the major effects of lipid peroxidation on mitochondrial enzymes and bioenergetic functions, some aspects of the pathophysiology of lipid peroxidation are considered in connection with maturation of reticulocytes, alternative oxidase of plant mitochondria, aging, and ischemia-reperfusion syndrome. The final part of the article is devoted to the regulation and control of lipid peroxidation in mitochondria with particular emphasis to the role of the respiratory substrates.