The entire DNA sequence of the human mt genome - 16,569 nucleotides - was determined in 1981, well in advance of the Human Genome Project. The mt genome contains 37 genes, all of which are involved in the production of energy and its storage in ATP. Thirteen of these genes encode proteins involved in oxidative phosphorylation. The remaining genes encode tranfer RNAs (22 genes) and ribosomal RNAs (2 genes) that translate the proteins' genes within the mitochrondrion. Mammalian mt genes use a slightly different genetic code than nuclear genes, where UGA = tryptophan, AUA = methionine, and AGA and AGG = stop.

Genes take up the majority of the mt genome. However, a noncoding region of approximately 1,200 nucleotides spans both sides of the arbitrary "0" position of the mt genome and goes by three confusing terms: control region, D-loop, and hypervariable region. Control region refers to the fact that this region contains the signals that control RNA and DNA synthesis. A single promoter on each DNA strand initiates transcription in each direction, and a single origin initiates replication of each strand. D-loop refers to the early phase of replication, when the first newly-synthesized strand displaces one of the parental strands, forming a "bubble" or loop. The DNA sequence of the control region is termed hypervariable, because it accumulates point mutations at approximately 10 times the rate of nuclear DNA.