The cysteinyl leukotrienes, namely leukotriene (LT)C₄ and its metabolites LTD₄ and LTE₄, the components of slow-reacting substance of anaphylaxis^,, are lipid mediators of smooth muscle constriction^,, and inflammation^,, particularly implicated in bronchial asthma^,. LTC₄ synthase (LTC₄S), the pivotal enzyme for the biosynthesis of LTC₄ (ref. ), is an 18-kDa integral nuclear membrane protein^, that belongs to a superfamily of membrane-associated proteins in eicosanoid and glutathione metabolism that includes 5-lipoxygenase-activating protein, microsomal glutathione S-transferases (MGSTs), and microsomal prostaglandin E synthase 1 (ref. ). LTC₄S conjugates glutathione to LTA₄, the endogenous substrate derived from arachidonic acid through the 5-lipoxygenase pathway. In contrast with MGST2 and MGST3 (refs , ), LTC₄S does not conjugate glutathione to xenobiotics. Here we show the atomic structure of human LTC₄S in a complex with glutathione at 3.3 Å resolution by X-ray crystallography and provide insights into the high substrate specificity for glutathione and LTA₄ that distinguishes LTC₄S from other MGSTs. The LTC₄S monomer has four transmembrane α-helices and forms a threefold symmetric trimer as a unit with functional domains across each interface. Glutathione resides in a U-shaped conformation within an interface between adjacent monomers, and this binding is stabilized by a loop structure at the top of the interface. LTA₄ would fit into the interface so that Arg 104 of one monomer activates glutathione to provide the thiolate anion that attacks C6 of LTA₄ to form a thioether bond, and Arg 31 in the neighbouring monomer donates a proton to form a hydroxyl group at C5, resulting in 5(S)-hydroxy-6(R)-S-glutathionyl-7,9-trans-11,14-cis-eicosatetraenoic acid (LTC₄). These findings provide a structural basis for the development of LTC₄S inhibitors for a proinflammatory pathway mediated by three cysteinyl leukotriene ligands whose stability and potency are different and by multiple cysteinyl leukotriene receptors whose functions may be non-redundant.