Thermally assisted hydrolysis and methylation-gas chromatography (THM-GC) is an important tool to analyse fatty acid in complex matrices. Since THM-GC has major drawbacks such as isomerisation when applied to fatty acids in natural matrices, a direct thermal desorption (DTD) interface and an incubation time of 30 min were used to circumvent these problems. Using vegetable oils such as sunflower oil and triarachidonin, the conversion of triglycerides into their fatty acid methyl esters (FAMEs) was investigated. The yields using a DTD (and trimethylsulfonium hydroxide as a reagent) were found to be similar or even higher than when applying a conventional off-line method, while the FAME profiles were identical. When the procedure was applied to analyse the FAME profiles of microbial cells in a methanolic or aqueous suspension, it was found that accurate profiles are obtained for such samples. Thus, the present approach opens the route to analyse fatty acids in microbial cells in a fully automated fashion, which will allow high sample throughput. © 2002 Elsevier Science B.V. All rights reserved.