Disparities in minor histocompatibility antigens between HLA-matched organ and bone marrow donors and recipients create a potential risk for graft failure and graft-versus-host disease. These conditions necessitate lifelong pharmacological immunosuppression of organ and bone marrow transplant recipients. Recent technical advances have resulted in the identification of the chemical nature of the first human minor histocompatibility antigens. A new era of research has begun to provide insights into the genetics of minor antigens and their putative role in transplantation.