Duchenne muscular dystrophy (DMD) is caused by mutations that impair normal production of dystrophin in muscle and brain tissues. The dystrophin gene is expressed at extremely low levels in both humans and mice, which makes analysis of the 14kb mRNA a difficult task. In addition, 30% of all cases of DMD (and the genetic lesion in all three known mdx mouse models for DMD) are thought to arise from single base mutations, yet methods are not available to routinely identify and analyze these mutations and their effects on disease progression. We have been using the polymerase chain reaction (PCR) to analyze the expression of the murine dystrophin gene. A simple assay is described that distinguishes the murine dystrophin transcripts expressed from either the muscle or brain promoter. In addition, amplification of overlapping segments from the 5' end of the murine transcript has enabled the identification of DNA sequence variations between wild-type and mdx mice. These results demonstrate that the mutation in the original strain of mdx mice is distinct from those in two newer mdx isolates and that three independently isolated mdx mutants are available for study of DMD.