Vertebrate group XII phospholipases A(2) (GXII PLA(2), conserved domain pfam06951) are proteins with unique structural and functional features within the secreted PLA(2) family. In humans, two genes (GXIIA PLA(2) and GXIIB PLA(2)) have been characterised. GXIIA PLA(2) is enzymatically active whereas GXIIB PLA(2) is devoid of catalytic activity. Recently, putative homologues of the vertebrate GXII PLA(2)s were described in non-vertebrates. In the current study a total of 170 GXII PLA(2) sequences were identified in vertebrates, invertebrates, non-metazoan eukaryotes, fungi and bacteria. GXIIB PLA(2) was found only in vertebrates and the searches failed to identify putative GXII PLA(2) homologues in Archaea. Comparisons of the predicted functional domains of GXII PLA(2)s revealed considerable structural identity within the Ca(2+)-binding and the catalytic sites among the various organisms suggesting that functional conservation may have been retained across evolution. The preservation of GXII PLA(2) family members from bacteria to human indicates that they have emerged early in evolution and evolved via gene/genome duplication events prior to Eubacteria. Gene duplicates were identified in some invertebrate taxa suggesting that species-specific duplications occurred. The analysis of the GXII PLA(2) homologue genome environment revealed that gene synteny and gene order are preserved in vertebrates. Conservation of GXII PLA(2)s indicates that important functional roles involved in species survival and were maintained across evolution and may be dependent on or independent of the enzyme's phospholipolytic activity.