We report a novel, highly sensitive and selective method for the detection and quantification of acyl-CoA esters from Arabidopsis thaliana. Extracted acyl-CoA esters were derived to their fluorescent acyl-etheno-CoA esters, separated by ion-paired reversed-phase HPLC, and detected fluorometrically. We report the composition and concentration of the acyl-CoA pool in mature A. thaliana leaves, and during storage-lipid breakdown in 2-day-old seedlings. The concentrations measured were in the 1-4 microM range for both tissue types. To our knowledge, this is the first time that reliable estimates of acyl-CoA ester concentrations have been made for plants.