Autoxidation of polyunsaturated fatty acids and esters leads to a complex mixture containing hydroperoxides and cyclic peroxides. The oxidation mixture of cholesteryl arachidonate, which has been characterized by a variety of mass spectrometry techniques, was subject to analysis by conventional thiobarbituric acid-reactive substance (TBARS) and ferrous oxidation in xylenol orange (FOX) assays. Our results indicate that the FOX assay is not specific for hydroperoxides. Cyclic peroxides, such as monocyclic peroxides and serial-cyclic peroxides, give a positive FOX response even after triphenylphosphine reduction. We suggest that bicyclic endoperoxides are the major TBARS active compounds present in cholesteryl arachidonate oxidation mixtures. These compounds give a positive FOX assay before reaction with triphenylphosphine but negative TBARS and FOX assays after this reaction. Caution should be exercised when the FOX assay is used to analyze highly oxidized lipids, especially arachidonyl-containing lipids.