We performed cross-species hybridization at the major histocompatibility complex (MHC) to evaluate the ability of murine probes to reveal polymorphism in wild meadow vole populations. Genomic hybridization of a mouse MHC class II I-Aα cDNA revealed extensive restriction fragment length polymorphisms when meadow vole genomic DNA was cleaved with BamHI EcoRI, HindIII, or HincII. The polymorphisms were interpreted by analyzing 10 half-sib families, comprising 6 sires, 10 dams, and 34 offspring. At least 26 different alleles were found with HincII in the family material, and the estimated heterozygosity at those sites is 96%. Several other alleles were found in a population sample. The high degree of genetic variation revealed by this system indicates that it is a viable alternative to multilocus "genetic fingerprinting" probes for the analysis of small mammal pedigrees or strains. Several mouse MHC probes are readily available and they provide a quick route to screening populations and remove the need to extract species-specific markers from genomic libraries.