Cucumber seedlings associated with the arbuscular mycorrhizal (AM) fungi Glomus WUM10 or G. caledanium (BEG 15) were grown in PVC tubes with a lateral root-free compartment and an identical compartment containing both hyphae and roots. The amounts of specific fatty acids, in the neutral lipid and phospholipid fractions, were measured in both compartments and compared with controls without mycorrhiza. The phospholipid fatty acids (PLFAs) 16:1 omega 5, 18:1 omega 7c, 20:4 and 20:5 were present in higher amounts in soil with mycorrhizal hyphae than in soil without mycorrhizal hyphae. The largest relative difference was found in 20:5, but a good correlation existed between 16:1 omega 5 and 20:5 in soil with hyphae. Amounts of these fatty acids were correlated both with length of mycorrhizal hyphae and with amounts of ATP in soil. Conversion factors to calculate hyphal length and AM fungal biomass carbon using the phospholipid fatty acids could thus be estimated; 38 nmol PLFA 16:1 omega 5 mg(-1) AM fungal biomass C (Glomus WUM10) and 22 nmol PLFA 20:5 mg(-1) biomass C. The fatty acid 16:1 omega 5 from the neutral lipid fraction, containing triglycerides, dominated in soils with mycorrhizal hyphae. The amount of 16:1 omega 5 in the neutral lipid fraction decreased during storage of soils, indicating a decrease in storage lipids, while the proportion of 16:1 omega 5 in the phospholipid fraction was almost unaffected.