The lipid and fatty acid compositions of Glomus intraradices and G. claroideum mycelia, extracted from quartz sand in a compartmentalized growth system, were analysed. The fungi were grown in association with Cucumis sativus and Trifolium subterraneum, respectively. For both fungi, the fatty acids 16:1 omega 5 and 16:0 dominated in the neutral lipid fraction, and 18:1 omega 7 made up a significant part of the phospholipids. The fatty acids were used as estimators of the amount of neutral lipids and phospholipids of AM fungi as well as to calculate the biomass of different parts of their mycelium. The phospholipid content was higher in hyphae than in spores, whereas the opposite was observed for neutral lipids. In 3-mo-old G. intraradices mycelium, spores accounted for 90% of the external biomass, and calculations indicated that about 20% of the spore biomass consisted of neutral lipids. In both fungi the fatty acid compositions of hyphae and spores were similar regardless of the age of the mycelium. Using the signature fatty acid 16:1 omega 5 to calculate the distribution of AM biomass for a 2-mo-old mycelium of G. claroideum, we found that the fungal biomass was equally distributed between the external mycelium and the internal mycelium in the host root.