Graft rejection or graft-versus-host (GVH) disease after HLA-identical stem cell transplantation is the result of recognition of minor histocompatibility antigens (mHags) by immunocompetent T lymphocytes from recipient or donor origin, respectively. Cytolytic T lymphocyte (CTL) clones can be isolated during graft rejection and GVH disease to identify mHags and their corresponding genes. Thus far, all human mHags identified appeared to be HLA class I–restricted. Here, we report the characterization of the first human HLA class II–restricted sex-linked mHag involved in GVH disease. Previously, we isolated an HLA-DQ5–restricted CD4⁺ CTL clone from a male patient with chronic myeloid leukemia who developed acute GVH disease grade III-IV after transplantation of HLA genotypically identical female stem cells. Using a panel of female HLA-DQ5⁺ EBV cells that we stably transfected with Y chromosome–specific genes, we determined that the HLA class II male-specific mHag (H-Y) was encoded by the Y chromosome–specific gene DBY. The H-Y epitope was localized in the DBY protein using female HLA-DQ5⁺peripheral blood mononuclear cells loaded with DBY protein fragments. The minimal peptide sequence leading to maximal recognition by the specific HLA-DQ5–restricted CTL clone was characterized as the 12–amino acid sequence HIENFSDIDMGE. Although the epitope differed by 3 amino acids from its X-homolog DBX, only 2 polymorphisms were shown to be essential for recognition by the CTL clone.