Oxidative stress has been implicated in development of a wide variety of disease processes, including cardiovascular disease, cancer, and neurodegenerative diseases, as well as progressive and normal aging processes. Isoprostanes (IsoPs) are prostaglandin-like compounds that are generated in vivo from lipid peroxidation of arachidonic acid (AA, C20:4, ω-6) and other polyunsaturated fatty acids (PUFA). Since the discovery of IsoPs by Morrow and Roberts in 1990, quantification of IsoPs has been shown to be excellent biomarkers of in vivo oxidative damage. Eicosapentaenoic acid (EPA, C20:5, ω-3) is the most abundant PUFA in C. elegans and gives rise to F3-IsoPs upon nonenzymatic free radical-catalyzed lipid peroxidation. The protocol presented is the current methodology that our laboratory uses to quantify F3-IsoPs in C. elegans using gas chromatography/mass spectrometry (GC/MS). The methods described herein has been optimized and validated to provide the best sensitivity and selectivity for quantification of F3-IsoPs from C. elegans lysates.