The efficient microscale synthesis of [1-14C]propionyl-CoA from commercially available sodium [1-14C]-propionate using 1,1'-carbonyldiimidazole in yields of nearly 70% is reported for the first time. A substantial improvement in the process for making [1-14C]acetyl-CoA from sodium [1-14C]acetate was also achieved. Yields of greater than 90% were consistently obtained for the latter synthesis. The salt-free CoA-thioesters were obtained in homogenous form by reverse-phase HPLC. The products were judged to be pure by 1H NMR analysis: neither iso-CoA analogs nor contaminants frequently found in commercial samples could be detected. The samples of acetyl- and propionyl-CoA were shown to be radiochemically pure by HPLC and by analysis of the products of incubations with acetyl- and propionyl-CoA carboxylase. This highly efficient synthesis is a cost-effective method for the preparation of radiolabeled CoA thioesters and can easily be adapted to the production of other acyl-CoA analogs.