The graft-versus-host disease (GVHD) seen in human leukocyte antigen (HLA)-matched sibling bone marrow transplants is by definition due to the "minor" histocompatibility antigens (mHAs) encoded outside the HLA region of human chromosome 6. Few of these antigens have been characterized in humans, and in general the locations of the encoding loci are unknown. Genetic experiments performed in mice have identified many mHAs, but only a few genes have been identified. Using T lymphocyte clones reactive with specific mHAs, combined with genetic linkage analysis, we identified two distinct loci in a single patient, each locus encoding an antigen presented to a T cell clone by HLA-B7. The technique used in this study should allow a rough enumeration of the number of mHAs in humans that are capable of eliciting T cell responses in vivo. Whether these T cell responses correlate with clinical GVHD is not yet clear.