Although the DNA in individuals within the same species is typically greater than 99% similar, there are regions of the DNA that are individually specific. These regions often contain repeating sequences of nucleic acids (bases), and are subject to the accumulation of mutations - either changes in the number of repeats or in the bases themselves - at a much higher rate than in the gene (in which an accumulation of too many mutations would be lethal). Though there are mutations generated with new individual, many of the repeating patterns are inherited directly from the parents, thus making these highly variable regions ideal for individual identification and for determining parentage.

The genome contains sequences of bases that code for making proteins - the genes - but these regions make up less than 5% of the total DNA. The other regions of the genome serve a variety of purposes such as regulatory control or structural integrity. In the case of satellite DNA - segments often used for DNA fingerprinting - these regions are revealing themselves to play a role in maintaining the structure of the chromosome, as determined by the study of aging. In other cases, the sequence resembles existing genes, and are suspected as being ancient remnants of genes that were duplicated and diverged, and are now defunct. In most however, the DNA has no known purpose.

The first application of DNA forensics evidence was carried out by Alec Jefferies in 1983, in a British court case which sought to identify the relationship between an emigrant and her son. Dr. Jefferies had discovered a way to view minisatellite DNA regions which can differ greatly in length due to the number of repeats. This repeating sequence occurs many times throughout the genome and is believed to be generated through uneven crossing over and subsequent rearrangements in chromosomes. The result is a pattern of repeating segments that is unique in number and location in the genome of each individual.

Using a combination of electrophoresis , Southern-blotting , and a unique set of probes specific to the repeating unit, Jefferies developed the technique of multi-locus probe testing, patented as "DNA fingerprinting", though the term DNA fingerprinting is now widely applied to a variety of related techniques that target a number of repeating units.

Since then, similar sequences have been identified in an abundant number of animal and plant species, opening the door for DNA forensic applications on issues involving organisms other than humans. In the same way that DNA sequencing is used to differentiate one human from another in criminal investigations, it can accurately determine the species of an animal (or animal part), match an individual to a population, and identify parentage.