Myocardial mitochondria (MCh), isolated with rotenone (MCh + RO) and in absence of rotenone (MCh - RO), were studied in rabbits with ischemia (0.5 hr autolysis) and in controls. Content of acyl-CoA was increased by 50%, linoleic acid - by 49% and lysophosphatidyl choline - by 37% in MCh + RO of control animals as compared with the MCh - RO preparation. In the MCh + RO preparation from rabbits with ischemia content of acyl-CoA was increased by 62%, while concentration of free fatty acids (FFA) and phospholipids was similar to those of the MCh - RO preparation. After isolation of mitochondria with rotenone composition of adenine nucleotides was distinctly altered. Content of ATP was decreased by 27% in mitochondria of both ischemic and control animals, although total amount of adenine nucleotides was decreased only slightly. As shown by estimation of succinate oxidation and membrane potential rotenone did not affect the mitochondrial respiration. In mitochondria of ischemic rabbits concentrations of FFA and lysophosphatidyl choline were increased, whereas content of ATP, total amount of adenine nucleotides, the rate of succinate oxidation and membrane potential were decreased. The method developed, isolation of mitochondria with rotenone, may be used in studies of the role of acyl-CoA in energy metabolism of cells.