To accommodate the increasing need for [1-11C]fatty acids for use in routine medical studies and the large amounts of radioactivity required, a more advanced automated synthesis system for the preparation of [1-11C]fatty acids has been constructed. The synthesis of [1-11C]fatty acids has been completely automated using a new separation unit (isobaric Sepaltor) for the extraction procedure, which had caused some difficulties with automation. The yield of [1-11C]palmitic acid was 20-30 mCi, and that of 3-methyl [1-11C]heptadecanoic acid was 2-7 mCi. The time required for the synthesis was less than 30 min from the start of the 11CO2 trapping. This system has been used for more than 20 preparations of [1-11C]palmitic acid and more than 20 preparations of 3-methyl [1-11C]heptadecanoic acid.