House mice (Mus domesticus) communicate using scent-marks, and the chemical and microbialcomposition of these ‘extended phenotypes’ are both influenced by genetics. This study examined howthe genes of the major histocompatibility complex (MHC) and background genes influence the volatilecompounds (analysed with Gas Chromatography Mass Spectrometry or GC/MS) and microbialcommunities (analysed using Denaturating Gradient Gel Electrophoresis or DGGE) in scent-marksproduced by congenic strains of mice. The use of Consensus Principal Components Analysis isdescribed and shows relationships between the two types of fingerprints (GC/MS and DGGE profiles).Classification methods including Support Vector Machines and Discriminant Partial Least Squaressuggest that mice can be classified according to both background strain and MHC-haplotype. Asexpected, the differences among the mice were much greater between strains that vary at both MHCand background loci than the congenics, which differ only at the MHC. These results indicate that thevolatiles in scent-marks provide information about genetic similarity of the mice, and support the ideathat the production of these genetically determined volatiles is influenced by commensal microflora.This paper describes the application of consensus methods to relate two blocks of analytical data.