Polyunsaturated fatty acids (PUFA) are important constituents in all eukaryotic organisms, contributing to the structural integrity of biological membranes and serving as precursors for enzymatically-generated local hormones. In addition to these functions, PUFA can generate by a free radical-initiated mechanism, key products which participate in a variety of pathophysiological processes. In particular, free radical-catalyzed peroxidation of PUFA leads to in vivo formation of isoprostanes (IsoP), neuroprostanes (NeuroP), and phytoprostanes (PhytoP) which display a wide range of biological actions. IsoP are now the most reliable indicators of oxidative stress in humans. In this review, we will discuss some advances in our knowledge regarding two cyclic PUFA derivatives, IsoP and PhytoP, and how their biological roles may be clarified through new approaches based on analytical and synthetic organic chemistry.