We have mapped the multiple (15-25) genes coding for the hormonally regulated major urinary proteins (MUPs) of the mouse by using a cloned cDNA probe. By Southern blot analysis of DNA from Chinese hamster-mouse somatic cell hybrids, all of the MUP genes were found to be on chromosome 4. Different inbred mouse strains showed DNA polymorphism in their MUP Southern hybridization pattern. Analysis of recombinant inbred strains derived from these parent strains has shown that all the polymorphisms are linked to the MUP-a locus on chromosome 4. The combination of these mapping techniques should be applicable to many cloned DNA sequences.