To explore the pathogenic mechanism of GVHD, attempting to forecast the degree of GVHD after stem cell transplantation, and to enhance the therapeutic effectiveness of clinical transplantation. The conventional microlymphocytotoxicity and sequencing methods were used in typing the HLA. The degrees of GVHD were estimated by molecular modeling of HLA antigens and veryfied the estimation by comparing the clinical results with anticipated degrees. In 8 recipients, three were transplanted with half matched stem cells. Among these 3 pationts, two developed IV degree GVHD, and one developed II degree GVHD. In the other 3 patients, cells of two unmatched HLA antigens were transplanted, and among them one developed I degree GVHD, and two developed II degree GVHD. In two patients who were transplanted with cells of one unmatched HLA antigens, I and II degrees GVHD developed respectively. Second, the correlationship analysis showed that degrees of GVHD had positive correlation with the RMSD (relative mean square deviation) between different HLA antigens. These results indicated that the degrees of GVHD after stem cell transplantation were related with the difference of three dimensional structures of unmatched stem cell HLA antigens; molecular modeling might be used to predict the prognosis of clinical stem cell transplantation.