Quantification of eicosanoids and oxylipins derived from other polyunsaturated fatty acids in biological samples is crucial for a better understanding of the biology of these lipid mediators. Moreover, a robust and reliable quantification is necessary to monitor the effects of pharmaceutical intervention and diet on the arachidonic acid (AA) cascade, one of today's most relevant drug targets. Low (sub-nanomolar) concentrations and a large number of structurally similar analytes, including regioisomers, require high chromatographic resolution and selective and sensitive mass spectrometry analysis. Currently, reversed-phase liquid chromatography in combination with detection on sensitive triple-quadrupole instruments, operating in selected reaction monitoring mode, is the main method of quantitative oxylipin analysis. A lack of standardized sample collection, handling, and preparation procedures, degradation of the analytes during sample preparation, and purity and availability of standards (internal standards) are the major problems of targeted metabolomics approaches for the AA cascade. Major challenges for instrumental analytical methods are the detection of esterified oxylipins, and separation and individual detection of oxylipin isomers. Solving these problems would help to further knowledge of the biology of lipid mediators, and is an important task for bio-analytical research.