Mast cells and basophils degranulate upon activation, releasing preformed mediators from intracellular granules into the extracellular environment, of which tryptase and histamine are the two most common and best characterized mediators. Despite the large number of mediators synthesized by mast cells, the non-tryptase biomarkers used to evaluate systemic mastocytosis and mast cell activation syndrome do not include the metabolites of the prestored amine histamine and the de novo synthesized phospholipids prostaglandin D2 and leukotriene C4. Currently, these markers are not used as criteria for the diagnosis of mastocytosis and mast cell activation syndrome. However, consensus groups foster the use of increases in measured baseline levels of these metabolites as potential diagnostic criteria. Metabolites of arachidonic acid such as prostaglandin D2 or leukotriene C4 play a role in the development of symptoms in systemic mastocytosis and mast cell activation syndrome. In this review, the metabolites of arachidonic acid and the detection of the metabolites of leukotrienes and prostaglandins in mastocytosis are highlighted. Measurement of these metabolites remains a major challenge because they are not widely available in daily clinical practice. However, new insights have been gained in recent years, and their application in the clinic has progressed.