The genes of the major histocompatibility complex (MHC) are highly polymorphic loci that encode cell surface proteins, class I and II molecules. They present peptide antigens to T cells and thereby control immunological self/nonself recognition. Increasing evidence indicates that MHC genes also influence odor and mating preferences; however, it is unclear how. Here we report the results of chemical analyses of male mouse urinary odors collected from a variety of mouse strains, including MHC-congenics, recombinants, mutants, and transgenics (i.e., beta2 microglobulin "knockouts," which lack class I expression, and transporters associated with antigen processing (TAP) knock-outs). After the identification of volatile odor components by gas chromatography/mass spectrometry, the odor profiles of urine samples were analyzed quantitatively by using stir bar sorptive extraction and gas chromatography/atomic emission detection. Results showed that MHC genes influenced the amounts of testosterone-mediated pheromones, sulfur-containing compounds, and several carbonyl metabolites. This is the first report to quantitatively link known mouse pheromones to classical, antigen-binding MHC loci. Surprisingly, these compounds were not influenced by TAP genes, even though these loci are MHC-linked and play a role in peptide presentation. Whereas identification of MHC-determined odorants does not reveal their metabolic origin, some constituents were also present in blood serum, and their levels were not altered by antibiotics.