Bioactive lipid mediators derived from polyunsaturated fatty acids (PUFA) exhibit a range of tissue- and cell-specific activities in many physiological and pathological processes. Electrospray ionisation tandem mass spectrometry coupled to liquid chromatography (LC/ESI-MS/MS) is a sensitive, versatile analytical methodology for the qualitative and quantitative analysis of lipid mediators. Here we present an LC/ESI-MS/MS assay for the simultaneous analysis of twenty mono- and poly-hydroxy-fatty acid derivatives of linoleic, arachidonic, eicosapentaenoic and docosahexaenoic acids. The assay was linear over the concentration range 1–100 pg/µL, whilst the limits of detection and quantitation were 10–20 and 20–50 pg, respectively. The recovery of the extraction methodology varied from 76–122% depending on the metabolite. This system is useful for profiling a range of biochemically related potent mediators including the newly discovered resolvins and protectins, and their precursor hydroxyeicosapentaenoic and hydroxydocosahexaenoic acids, and, consequently, advance our understanding of the role of PUFA in health and disease. Copyright © 2007 John Wiley & Sons, Ltd.