A kinetoplast is a network of circular DNA (called kDNA) inside a mitochondrion that contains many copies of the mitochondrial genome. The most common kinetoplast structure is a disk, but they have been observed in other arrangements. Kinetoplasts are only found in Excavata of the class Kinetoplastida. The variation in the structures of kinetoplasts may reflect phylogenic relationships between kinetoplastids. A kinetoplast is usually adjacent to the organism's flagellar basal body, suggesting that it is bound to some components of the cytoskeleton. In Trypanosoma brucei this cytoskeletal connection is called the tripartite attachment complex and includes the protein p166.

In trypanosomes, a group of flagellated protozoans, the kinetoplast exists as a dense granule of DNA within the mitochondrion. Trypanosoma brucei, the parasite which causes African trypanosomiasis (African sleeping sickness), is an example of a trypanosome with a kinetoplast. Its kinetoplast is easily visible in samples stained with DAPI, a fluorescent DNA stain, or by the use of fluorescent in situ hybridization (FISH) with BrdU, a thymidine analogue. Another parasite in the genus, Trypanosoma cruzi, causes Chagas disease in humans (primarily in Central and South America), which is transmitted through the kissing bug. Although African sleeping sickness is more dangerous than Chagas disease, the kinetoplast of T. cruzi is significantly larger than that of T. brucei. Trypanosoma equiperdum causes the disease dourine in horses, and is the only sexually transmitted trypanosome infection. The kinetoplasts of T. equiperdum are unique in that every minicircle has the same genetic sequence.

Purified kinetoplast DNA from Crithidia fasciculata is sold by two biochemical companies, TopoGen and Inspiralis. The kinetoplast DNA is used as a substrate to test the functionality of drugs or toxins targetting Topoisomerase II, a protein associated with cell division that can untangle DNA by passing strands through each other. Since kinetoplasts are normally too large to move through agar gel, the appearance of bands associated with minicircles during a gel electrophoresis assay indicate that Topoisomerase II has decatenated the kinetoplasts. This assay can be used to determine whether drugs or toxins that target Topoisomerase II are present. Kinetoplasts from C. fasciculata are also used in biophysical studies of kinetoplast DNA as a natural example of an Olympic gel.

The kinetoplast contains circular DNA in two forms, maxicircles and minicircles. Maxicircles are between 20 and 40kb in size and there are a few dozen per kinetoplast. There are several thousand minicircles per kinetoplast and they are between 0.5 and 1kb in size. Maxicircles encode the typical protein products needed for the mitochondria which is encrypted. Herein lies the only known function of the minicircles - producing guide RNA (gRNA) to decode this encrypted maxicircle information, typically through the insertion or deletion of uridine residues. The network of maxicircles and minicircles are catenated to form a planar network that resembles chain mail. Reproduction of this network then requires that these rings be disconnected from the parental kinetoplast and subsequently reconnected in the daughter kinetoplast. This unique mode of DNA replication may inspire potential drug targets.

The best studied kDNA structure is that of Crithidia fasciculata, a catenated disk of circular kDNA maxicircles and minicircles, most of which are not supercoiled. Exterior to the kDNA disk but directly adjacent are two complexes of proteins situated 180˚ from each other and are involved in minicircle replication. The network topology of kinetoplast DNA is primarily understood from experiments on C. fasciculata, based on gel electrophersis of kinetoplasts that have been broken down by restriction enzymes. These experiments indicate that each minicircle is linked to three on average, and that the crystal lattice structure most consistent with the data is the honeycomb lattice. More recent studies based on atomic force microscopy have corroborated the trivalent connectivity, but have shown that the structure is highly disordered.

Variations of kinetoplast networks have also been observed and are described by the arrangement and location of their kDNA.

The presence of this variety of kDNA structures reinforces the evolutionary relationship between the species of kinetoplastids. As pan-kDNA most closely resembles a DNA plasmid, it may be the ancestral form of kDNA.

The replication of the kinetoplast occurs simultaneously to the duplication of the adjacent flagellum and just prior to the nuclear DNA replication. In a traditional Crithidia fasciculata kDNA network, initiation of replication is promoted by the unlinking of kDNA minicircles via topoisomerase II. The free minicircles are released into a region between the kinetoplast and the mitochondrial membrane called the kinetoflagellar zone (KFZ). After replication the minicircles migrate by unknown mechanisms to the antipodal protein complexes that contain several replication proteins including an endonuclease, helicase, DNA polymerase, DNA primase, and DNA ligase, which initiate repair of remaining discontinuities in the newly replicated minicircles.