Lipid mediators derived from essential fatty acids such as arachidonic acid play important and sometimes pivotal roles in physiologic and pathophysiologic processes. Prostaglandins, thromboxane and leukotrienes are well-known eicosanoids that play a role in hemodynamics and inflammation. More recently, new families of mediators were uncovered that constitute a new genus that stimulate resolution of acute inflammation, are organ-protective and reduce the sequelae of ischemia-reperfusion tissue injury. These include the resolvins (E-series and D-series), protectins (neuroprotectin D1/protectin D1) and maresins biosynthesized from omega-3 essential fatty acids. Phagocytes play a major role in tissues and have a high capacity to produce these mediators, which depend on their tissue and state of activation. Since metabolomic profiling of these biosynthetic pathways in phagocytes can also yield inactive metabolites as well as isomers of specific mediators, it is important to select appropriate methods for identifying target mediators and pathway biomarkers. In this chapter, we review state-of-the-art approaches to identify and profile eicosanoid and docosanoid pathways, including specialized pro-resolving mediators such as resolvins, protectins and maresins that are produced by phagocytes in inflammatory exudates. We provide protocols for isolation and criteria for selecting methods and give examples of metabolomics and lipidomic procedures using liquid chromatography-tandem mass spectrometry-based instrumentation. The approaches reviewed here can provide documentation of bioactive mediators from the eicosanoid and docosanoid-metabolomes in relation to their biosynthesis and inactivation by phagocytes, particularly neutrophils and macrophages.