Abstract: Two pairs of HLA from donor and recipient of bone marrow allotransplantation with severe graft versus host disease (GVHD) were selected to perform structure modeling and comparison each other. The differences among these HLA proteins were found in surface conformation modeled by computer, Which were the main factors to prime GVHD after transplantation.It was suggested that the computerized modeling and comparing of HLA from donor and recipient might be used to prognose GVHD.