A new assay method for fatty acid synthetase using mass fragmentography is described. The amounts of fatty acids synthesized in deuterated water are determined by mass fragmentography by monitoring the intensities of m/e 77 and m/e 74 fragment ions using heptadecanoic acid as an internal standard. This method is suitable for any fatty acid synthetase which produces several species of fatty acids and is also applicable to crude enzyme preparations. This procedure is more sensitive and specific than the conventional spectrophotometric method. Fatty acid synthetases from rat liver and Brevibacterium ammoniagenes are analyzed by this method.