I demonstrate a new method to detect specifically mutant mitochondrial DNA (mtDNA) with the deletion. I designed an oligonucleotide probe that was designated the "ATP8/ND5 Chimera" probe. By Southern blot analysis, this probe specifically detected the deleted mtDNA. The specificity of the probe was further confirmed by in situ hybridization. In tissues where multiple deleted mtDNAs were detected, such as muscle tissues from a patient with myotonic dystrophy and from an aged individual, the in situ hybridization detected a small number of muscle fibers that had the deleted mtDNA. These results indicate that in situ hybridization using this probe is a useful and specific method for detecting a small amount of deleted mtDNA.