We have sequenced the 3'-untranslated region (3'-UTR) and first intron of six strains of Mus musculus, as well as M. spretus, M. castaneus, and M. shanghai. A marked degree of polymorphism was evident in the sequences, and among all of the strains, no two haplotypes were identical. Of particular note, insertional mutations modifying the 5'-TTATTTAT sequence in the 3'-UTR, which in its RNA form acts as a translational repressor, were observed in New Zealand White and M. spretus strains. The mutations that we have identified dictate several restriction-fragment length polymorphisms, which should be useful in following the tumor necrosis factor-encoding gene (TNF) in backcross analysis and in defining the ancestry of TNF in mice of indeterminate parentage. Moreover, the data provide a substrate for the future analysis of differences in the level of TNF expression by genetically distinct mice.