Fatty acid synthetase was isolated from guinea pig Harderian gland. This enzyme complex exhibited a unique character as compared with the fatty acid synthetase from the liver of the same animal. The former enzyme produced many odd-numbered and methyl-branched fatty acids in the presence of methylmalonyl-CoA. These fatty acids are characteristic components of the lipid secreted from this gland. The chemical structure of this lipid has been identified as 1-O-alkyl-2,3-diacylglycerol by previous work from this laboratory (Yamazaki, T., Seyama, Y., Otsuka, H., Ogawa, H., & Yamakawa, T. (1981) J. Biochem. 89, 683-691). Apparent Km values (5 X 10(-6) M) for acetyl-CoA and propionyl-CoA were the same, but the Vmax for propionyl-CoA was much higher than that for acetyl-CoA. The pI value of the fatty acid synthetase from Harderian gland was 5.3, and the molecular weight of the enzyme was 9 X 10(5) daltons. The beta-ketoacyl reductase had pro-S stereospecificity and the enoly reductase had pro-R stereospecificity for NADPH. The results presented in this paper indicate that the fatty acid synthetase from guinea pig Harderian gland can produce a set of fatty acids needed for the synthesis of the lipid secreted from this gland, and that the fatty acid synthetase has a characteristic organ specificity.