Mammalian secretory phospholipase A(2)s (sPLA(2)s) are classified into several groups according to molecular structure and the localization of intramolecular disulfide bridges. Among them, group IIA sPLA(2) has been thought to be one of the key enzymes in the pathogenesis of inflammatory diseases owing to its augmented expression under various inflammatory conditions. However, in a number of inbred mouse strains, the group IIA sPLA(2) gene is naturally disrupted by a frameshift mutation. Here, we report the cloning of a cDNA encoding a novel sPLA(2) expressed in the spleen of group IIA sPLA(2)-deficient mouse. We also cloned its human homolog and mapped its gene location on chromosome 1p36.12 near the loci of group IIA and V sPLA(2) genes. The human mature sPLA(2) protein consists of 125 amino acids (M(r) = 14,500) preceded by a 20-residue prepeptide and is most similar to group IIA sPLA(2) with respect to the number and positions of cysteine residues as well as overall identity (48%). Based on these structural properties, the novel sPLA(2) should be categorized into group II, called group IID to follow the already identified IIA to IIC sPLA(2)s. When the cDNA was expressed in COS-7 cells, PLA(2) activity preferentially accumulated in the culture medium. It is maximally active at neutral to alkaline pH and with 2 mM Ca(2+). In assays with individual substrates, L-alpha-1-palmitoyl-2-linoleoyl phosphatidylethanolamine was more efficiently hydrolyzed than the other phospholipids examined. An RNA blot hybridized with the cDNA exhibited two transcripts (2.0 and 1.0 kb) in human spleen, thymus, and colon. The expression of a novel sPLA(2) mRNA was elevated in the thymus after treatment with endotoxin in rats as well as in group IIA sPLA(2)-deficient mice, suggesting its functional role in the progression of the inflammatory process.