Genes of the major histocompatibility complex (MHC), which play a critical role in immune recognition, influence mating preference and other social behaviors in mice. Training experiments using urine scent from mice differing only in the MHC complex, from MHC class I mutants or from knock-out mice lacking functional MHC class I molecules (beta2m-deficient), suggest that these behavioral effects are mediated by differences in MHC-dependent volatile components. In search for the physical basis of these behavioral studies, we have conducted a comparison of urinary volatiles in three sub-strains of C57BL/6 mice, a beta2m-deficient mutant lacking functional MHC class I expression and two unrelated inbred strains, using the technique of sorptive extraction with polydimethylsiloxan and subsequent analysis by gas chromatography/mass spectrometry. We show (i) that qualitative differences occur between different inbred strains but not in mice with the C57BL/6 background, (ii) that the individual variability in abundance in the same mouse strain is strongly component-dependent, (iii) that C57BL/6 sub-strains obtained from different provenance show a higher fraction of quantitative differences than a sub-strain and its beta2m-mutant obtained from the same source and (iv) that comparison of the spectra of beta2m mice and the corresponding wild type reveals no qualitative differences in close to 200 major and minor components and only minimal differences in a few substances from an ensemble of 69 selected for quantitative analysis. Our data suggest that odor is shaped by ontogenetic, environmental and genetic factors, and the gestalt of this scent may identify a mouse on the individual and population level; but, within the limits of the ensemble of components analysed, the results do not support the notion that functional MHC class I molecules influence the urinary volatile composition.