In rabbit we observed heteroplasmy at an exceptionally high level, the heterogeneity occurring within the non-coding region of the DNA. Mitochondrial DNA (mt DNA) was cloned in pBR322 and the nucleotide sequence analysis of an EcoRI-Hind III fragment encompassing the non-coding region revealed that although there are common features with other mammalian mtDNAs (termed large central-conserved-sequence block, conserved-sequence blocks 1, 2 and 3 and termination-associated elements) the non-coding region shows an unusual organization; two stretches of tandem repeats of 20 bp and 153 bp are present in a part containing the origin of H-strand replication (OH) and probably the promoters for transcription as judged from other vertebrates. The long repeats are located between tRNA(Phe) and conserved sequence block 3 and the short repeats are located between conserved sequence blocks 1 and 2. When cloned in Escherichia coli (recA or recBC sbcb) DNA fragments containing the short repeats show length differences corresponding to various copy numbers of repeats. Electrophoretic analysis of the appropriate restriction fragments of rabbit mtDNA reveals extended intra- and inter-individual length heterogeneity. Both sets of repeats are involved in the generation of heterogeneity and are present in variable copy numbers from one mtDNA molecule to another. Moreover, rearrangement of the motives of the short repeat are observed to different extents in the mtDNA from one animal to another. The occurrence, maintenance and possible involvement of these repeated sequences, capable of forming stable secondary structures, are discussed in relation to their location in the region of control signals.