Isoprostanes (iPs) are free radical catalyzed prostaglandin isomers. Analysis of individual isomers of PGF 2␣-F2-iPs-in urine has reflected lipid peroxidation in humans. However, up to 64 F 2-iPs may be formed, and it is unknown whether coordinate generation, disposition, and excretion of F 2-iPs occurs in humans. To address this issue, we developed methods to measure individual members of the four structural classes of F 2-iPs, using liquid chromatography͞tandem mass spectrometry (LC͞MS͞MS), in which sample preparation is minimized. Authentic standards of F 2-iPs of classes III, IV, V, and VI were used to identify class-specific ions for multiple reaction monitoring. Using iPF 2␣-VI as a model compound, we demonstrated the reproducibility of the assay in human urine. Urinary levels of all F 2-iPs measured were elevated in patients with familial hypercholesterolemia. However, only three of eight F 2-iPs were elevated in patients with congestive heart failure, compared with controls. Paired analyses by GC͞MS and LC͞MS͞MS of iPF 2␣-VI in hypercholesterolemia and of 8,12-iso-iPF 2␣-VI in congestive heart failure were highly correlated. This approach will permit high throughput analysis of multiple iPs in human disease.