A novel procedure is described for the synthesis of acylcarnitines. This entails the synthesis of an N-acyl imidazole intermediate, which subsequently is reacted with L-carnitine perchlorate to form the acylcarnitine. The procedure is rapid and simple, and does not require a large excess of N-acyl imidazole to achieve a reaction yield of 50-70%. A procedure, based on reverse-phase Sep-Pak cartridges for rapid isolation of acylcarnitines from these reaction mixtures is also described. These procedures have, in particular, been applied in the synthesis of polyunsaturated acylcarnitines, including docosahexaenoylcarnitine.