Minor histocompatibility (H) loci encode alloantigens that are recognized by cytotoxic T (Tc) lymphocytes. A (C57BL/10 x 129)F1-derived transformed lymphocyte cell line was immunoselected in vitro with cloned Tc cells that were specific for H-3aa, a Chromosome 2-encoded minor H antigen. This cell line is heterozygous at H-3a (former symbol, Cd-1) and other loci. Three groups of antigen-loss variants were identified. One group contained mutations affecting only the antigen-encoding gene. Another group probably arose through a single homologous interchromosomal exchange, resulting in extensive regions of loss of heterozygosity (LOH). The third group of variants contained an interstitial LOH, one of which was shown to be a significant deletion. Several deletion boundaries were identified, one of which ordered the closely linked H-3a and beta 2-microglobulin (B2m) genes. We suggest that Tc immunoselection against minor H antigens is a promising approach for targeting negative selection to specified chromosomal regions and can provide high-resolution genetic map information.