A highly sensitive and specific method for the analysis of isoprotanes in vitro and in vivo is utilized. The methodology is based primarily upon capillary column gas chromatography (GC) negative ion chemical ionization (NICI)mass spectrometry (MS) or liquid chromatography (LC)/MS using stable isotope dilution techniques employing deuterated or [18O]-labeled internal standards. The assays offered are parent F2-isoprostanes and the major urinary isoprostane metabolite (2,3-dinor-5,6,-dihydro-15-F2t-IsoP,F2-isoprostane-M).