Cells made ischemic rapidly manifest many distinct structural and functional alterations as a consequence of the depletion of their energy stores. In attempting to determine which of these are causally related to the eventual cell death, the authors have emphasized the relationship to the reversibility of the ischemic injury. Two phenomena have consistently characterized irreversibly in contrast to reversibly injured ischemic cells: the inability to restore mitochondrial function and evidence of plasma membrane damage. Studies in the authors' laboratory are reviewed that have focused on the pathogenesis, biochemical nature, and the relationship to irreversible cell injury of both of these alterations. A number of mitochondrial abnormalities are related to changes in long-chain acyl-CoA metabolism with inhibition of adenine nucleotide translocation and potentiation of a Ca2+-dependent increase in the permeability of the inner mitochondrial membrane. These changes are reversible upon reoxygenation only when the large increase in intracellular Ca2+ content that accompanies the phospholipid depletion from other cellular membranes is prevented. This disorder in phospholipid metabolism is felt to be the critical lesion that produces irreversible cell injury in ischemia. It affects the endoplasmic and sarcoplasmic reticular membranes of liver and myocardial cells, respectively, and probably the plasma membranes of both. It is prevented by pretreatment with chlorpromazine. An activation of endogenous phospholipases by an elevated, cytosolic free Ca2+ ion concentration is suggested as the mechanism underlying this phospholipid disturbance. The central role of intracellular Ca2+ in the initiation and functional consequences of ischemic cell injury are emphasized.