A large body of evidence indicates that measurement of F2-isoprostanes, specific prostaglandin F2-like compounds derived from the non-enzymatic peroxidation of arachidonic acid, is a reliable biomarker of oxidant stress in the human body. Since the discovery of F2-isoprostanes in the early 1990s, a variety of analytical approaches has been introduced for the quantification of these novel compounds. The aim of the present review is to shed light on the available gas chromatographic-mass spectrometric assays for the measurement of plasma or urinary F2-isoprostanes and to highlight a number of issues which need to be addressed in order to implement F2-isoprostane measurement as a gold-standard biomarker of oxidative stress in biological samples.