The major histocompatibility complex (MHC) in the domestic cat was characterized using serological and molecular procedures. Reciprocal skin grafts were exchanged between unrelated cats; 75% of the skin grafts between the siblings of unrelated parents and 100% of those between the unrelated cats were acutely rejected within 14 days. Cytotoxic alloantisera were derived from 14 different individuals and were used in a population cluster analysis of unrelated feral cats to define overlapping immunogenetic specificities. In addition, pedigree analysis of the nine families in the NIH cat colony led to the description of allogeneic haplotypes which segregated from each other in family experiments. The data were used to derive the first feline MHC (termed FLA, feline leukocyte antigen) chart of detected haplotypes. Immunoprecipitation experiments using cytotoxic typing alloantisera identified both class I and class II type molecules. A molecular analysis of feline DNA using heterologous human or mouse molecular probes (class I and class II) revealed that the cat haploid genome contains approximately 20 class I loci and 2 class II genes. Class I genes of the domestic cat expressed limited restriction fragment length polymorphism (RFLP); approximately five times lower than the extent of RFLP observed in mice, rats, or pigs, and almost equivalent to the extent of MHC gene RFLP that is detected in humans and in the MHC- monomorphic Syrian hamster. Class I and class II genes were both genetically mapped to feline chromosome B2 using a panel of rodent x cat somatic cell hybrids. A partial cDNA class I gene (pFLA2) isolated from a cDNA library of a cat T-cell lymphoma cell line is presently under analysis.