Low energetic shift was found in liver mitochondria of rats with pneumonia, which was expressed as a decrease in rates of phosphorylating respiration and ADP phosphorylation independently on substrate of oxidation. Training of rats under hypoxic conditions led to a decrease in severity and distribution of inflammation in the animals with induced pneumonia. Patterns of mitochondrial oxidation, if Krebs cycle substrates were used, were normalized in most of the animals, while rates of ADP-stimulated respiration, phosphorylation as well as energy regulation of respiration and efficiency of phosphorylating respiration were distinctly increased. Alterations in mitochondrial energy reactions depended on the state of lipid peroxidation, initial steps of which may produce substrates of mitochondrial respiration. Training under hypoxic conditions, which protected against energy deficiency developed in pneumonia, contributed to increase in oxidative phosphorylation efficiency especially when lipid substrates were used.