To explore the cDNA and its genomic gene structure of human glycosylphosphatidylinositol specific phospholipase D (GPI-PLD), the stromal cells from human bone marrow were cultured, and the GPI-PLD cDNA was successfully cloned from stromal cells (GenBank Accession AY007546). After analyzing this cDNA, we found that it codes the signal peptide as well as the mature peptide (817 AA) of GPI-PLD. Compared with the cDNA cloned from human pancreas and liver, the homology of the cDNA is 99% and 95% respectively. After searching GenBank, we aligned the genomic gene of the GPI-PLD by DNATools software, and found that the GPI-PLD genomic gene was located in the human 6p22.1-22.3 and contained 25 exons, TATA box, CAAT box, enhancer and the sequence binding homo domain of Pit-1/GHF-1.