In human allogeneic bone marrow transplantation, graft-vs-host disease and graft rejection can occur even if the patient and donor are genotypically matched by inheritance for HLA. By definition, these allogeneic reactions are due to disparities in minor histocompatibility Ags (minor HAs). Minor HAs are presented to T lymphocytes as peptides bound to HLA molecules, and appear to be encoded by genes throughout the genome. We derived T lymphocyte clones from the PBL of a patient suffering from chronic graft-vs-host disease after bone marrow transplant from his HLA-identical sister. Clones reactive against minor HAs were selected on the basis of reactivity with pretransplant patient cells, and absence of reactivity with donor cells. One clone (MD2) was found to use HLA-B7 as a restricting element. A plasmid vector (pHEBo) containing cDNA encoding the HLA-B7 molecule was transfected into lymphoblastoid cell lines derived from two large families that previously had been saturation mapped for hundreds of polymorphic loci. When clone MD2 was tested against family K1362, it was found to be reactive with three of four grandparents, both parents, and eight of eleven offspring. The same clone was tested with family K1331, with two of three tested grandparents reactive, one of two parents, and nine of eleven offspring. Computer analysis showed that both family segregation patterns linked to an area on the long arm of chromosome 22, localizing the gene encoding this minor HA near the platelet-derived growth factor-beta and IL-2Rbeta genes.