Both the human and chimpanzee genomes have been mapped, with a 96% DNA sequence match between the two. Of the differences between the two genomes, 50% are due to single nucleotide polymorphisms (SNPs), sometimes called "point mutations". The other 50% are due to insertions/deletions (indels), most of which are caused by transposons and endogenous retroviruses.

Transposons are DNA elements capable of copying themselves from one part of the genome to another, sometimes with the aid of other transposons or viruses. In the past, transposons were labeled as "junk" DNA, as their function was unknown. It is now known that over 40% of the human genome is composed of transposons.

Endogenous retroviruses (ERVs), are virus genomes inserted in the human genome. ERVs represent about 8% of the total human genome. The vast majority of these viruses are mutated and can no longer function as viruses. However, a number of HRVs do retain the ability to copy themselves from one point of the genome to another, acting as a form of transposon. Some researchers have proposed that many transposons evolved from viruses, due to their highly similar DNA structure. HRVs have been found to modify human gene function in certain glandular tissue and the human placenta, as well as causing some human genetic diseases.

Most transposons and ERVs are common to both chimpanzees and humans. One self-replicating transposon, called LINE-1, appears to be very ancient and is present in animals prior to mammals. Most but not all LINE-1s are no longer able to transpose themselves due to point mutations.

A more recently evolved transposon family, the alu sequence group, has a million copies in the human genome. Alu transposons have incorporated themselves into many genes and perform regulation of these genes. The exact mechanism of regulation is unknown, but deletion of specific alus has been shown to alter gene expression. Alus can act both as gene silencers and enhancers. The vast majority of alus are common to both chimpanzees and humans, but several thousand are only found in humans.

Alu evolution appears to be currently active in modern humans. There are about 2000 alu sites in the human genome where one individual may differ from another. It is estimated that an alu change occurs roughly once in 200 births. Of the roughly one million alus common to chimpanzees and humans, nearly 99% occur in exactly the same DNA site in both genomes. Alus are found only in primates.

SVA elements are a very recent class of transposon almost entirely restricted to the human genome. There are several thousand SVAs in humans, only a handful of which match same-site SVAs in chimpanzees. SVAs appear to be a hybrid of LINE transposons combined with some viral genetic elements. SVAs, like alus, appear to associated with gene regulation and some human diseases. SVAs are currently evolutionarily active in human genomes, with a large number of polymorphisms in the modern human population.