A method for the determination of short-chain acyl-CoA esters in tissue extracts by HPLC has been developed. The acyl-CoA esters were extracted from freeze-clamped rat livers with perchloric acid. The extract was applied to a Sep-Pak C18 cartridge. The cartridge was washed with acidic water, pH 3, followed by petroleum ether, chloroform, and methanol. Then the acyl-CoA esters were eluted from the cartridge with ethanol/water (65:35) containing 0.1 M ammonium acetate. By this procedure, the acyl-CoA esters were concentrated and partially purified. The eluate was analyzed by HPLC using reverse-phase columns of Develosil ODS (0.46 X 15 cm plus 0.46 X 25 cm). The separation of the acyl-CoA esters was conducted with a linear gradient (1.75 to 10%) of acetonitrile. The CoA compounds (malonyl-CoA, succinyl-CoA plus CoASH, methylmalonyl-CoA, 3-hydroxy-3-methylglutaryl-CoA, acetyl-CoA, acetoacetyl-CoA, and propionyl-CoA) were identified and determined by monitoring at 260 nm. Isobutyryl-CoA was used as an internal standard, since the content of this CoA ester was negligible in livers from rats with several metabolic conditions. The lower limit of detection of individual acyl-CoA esters was approximately 50 pmol. Using this analytical method, short-chain acyl-CoA esters were determined in livers from normal and fasted rats.