Combinations of three extraction methods (modified Folch method, modified Bligh and Dyer and microwave-assisted extraction (MAE)) and two derivatization methods (alkaline methanolysis and derivatization with trimethylsulfonium hydroxide (TMSH)) are compared for determining phospholipid fatty acids (PLFAs) in soil and solid organic samples (animal manures, compost and vermicompost). The modified Folch method rendered the greatest total amount of PLFAs and the highest yields of individual PLFA biomarkers; the effect was most apparent in the vermicompost samples. MAE rendered similar extraction yields as the modified Bligh and Dyer method (the most commonly used extraction method), although MAE is much simpler and faster. The highest conversion yields of PLFAs into fatty acid methyl esters were achieved with TMSH as the derivatization agent. The modified Folch method together with derivatization with TMSH was the least complex and time consuming method of determining microbial community structure in solid environmental samples. (C) 2009 Elsevier Ltd. All rights reserved.