F-2-Isoprostanes are stable lipid peroxidation products of arachidonic acid, the quantification of which provides an index of oxidative stress in vivo. We describe a method for analysing isoprostaglandin F-2 alpha type III (19-F-2 alpha-IsoP) in biological fluids. The method involves solid-phase extraction on octadecyl endcapped and aminopropyl cartridges. After conversion to trimethylsilyl ester trimethylsilyl ether derivatives, isoprostaglandin F-2 alpha type III is analysed by mass spectrometry, operated in electronic impact selected ion monitoring mode. We have compared enzyme immunoassay (EIA; Cayman, Ann Arbor, MI, USA) to this method with 30 human urine aliquots following the same extraction procedure in order to determine the agreement between both methods. Isoprostaglandin F-2 alpha type III concentrations determined with gas chromatography-mass spectrometry (GC-MS) did not agree with those determined with EIA. Our results suggest that GC-MS and EIA do not measure the same compounds. As a consequence, comparison of clinical results using GC-MS and EIA should be avoided. (C) 2001 Elsevier Science B.V. All rights reserved.