A direct thermal desorption (DTD) interface was applied to profile the fatty acid composition of whole/intact aquatic micro-organisms using trimethylsulfonium hydroxide (TMSH) as derivatization reagent in a fully automated fashion without any sample treatment. DTD was used to release cellular free and esterified fatty acids, after conversion into their methyl esters, from the very limited amounts of cells available in plankton community analysis using fluorescence-activated cell sorting of mixed (natural) microbial/algal populations. The liner of the GC injector is used as a sample-and-reaction container with the aid of the DTD interface. The fatty acids are converted into their methyl esters after an incubation (hydrolysis) time of 30 min with TMSH. After transportation into the injector, the liner is heated to effect thermally assisted methylation. Simultaneously, the fatty acid methyl esters (FAMEs) are introduced from the liner into the capillary GC column. On the basis of peak intensities, the fatty acid compositions, thus obtained, were shown to be closely similar to those of a conventional lipid extraction and methylation procedure. The method was applied to some common freshwater algae, the green algae Scenedesmus acutus, the diatom Asterionella formosa and the filamentous cyanobacterium, Limnothrix sp. strain MRI. Using this novel method, poly-unsaturated fatty acids were methylated into their corresponding methyl esters without isomerization/pyrolytic side-reactions. The present method has been used to perform large series of analyses of algal and microbial cells. Up to 18 samples could be analysed per day. In order to reach this sample throughput, preparation of the (n + 1)th sample was performed simultaneously with GC analysis of the nth sample. © 2004 Elsevier B.V. All rights reserved.