Breeding the Y chromosome from certain Mus musculus domesticus strains onto the inbred laboratory mouse strain, C57BL/6J (B6), results in hermaphroditic progeny. This strain-dependent sex reversal suggests that there may be significant allelic variation in the murine sex determining gene, Sry. We have analysed the Sry genes from several domesticus-type Y chromosomes and show that they encode smaller proteins than the molossinus-type alleles SryB6 and Sry129. We have also identified a polymorphic stretch of trinucleotide repeats that is unique to strains causing sex reversal and show that specific changes in the predicted polyglutamine amino acid sequence at this site are associated with different degrees of sex reversal.