The measurement of F2-isoprostanes by methods utilizing mass spectrometry is widely regarded as the best currently available biomarker of lipid peroxidation. F2-isoprostanes and their metabolites can be measured accurately in plasma, urine, and other body fluids using mass spectrometric techniques, and detailed protocols have been published in several papers. However, many clinical studies and intervention studies with diets or supplements, have employed single "spot" measurements of F2-isoprostanes on either plasma/serum or urine to estimate "oxidative stress." This review examines the validity of the common assumption that plasma and urinary F2-isoprostane measurements are equivalent. It identifies scenarios where they may not be and where "spot" measurements can be misleading, with examples from the literature. We also discuss the controversial issue of whether and how F2-isoprostane levels in plasma should be standardized against lipids, and, if so, which lipids to use.