The cause of isolated missing teeth remains unclear, but the condition is believed to be associated with genetic or environmental factors during dental development. Missing teeth have been reported in association with increased maternal age, low birth weight, multiple births and rubella virus infection during embryonic life.

There is a possible correlation between tooth agenesis and innervation. A relationship was also postulated between abnormalities of the brainstem and the presence of agenesis.

Hypodontia is often familial, and can also be associated with genetic disorders such as ectodermal dysplasia or Down syndrome. Hypodontia can also be seen in people with cleft lip and palate.

Among the possible causes are mentioned genetic, hormonal, environmental and infectious.

Cause due to hormonal defects: idiopathic hypoparathyroidism and pseudohypoparathyroidism. Exists the possibility that this defect depends on a moniliasis (candidiasis, "candida endocrinopathy syndrome").

Environmental causes involving exposure to PCBs (ex.dioxin), radiation, anticancer chemotherapeutic agents, allergy and toxic epidermal necrolysis after drug.

Infectious causes of hypodontia: rubella, candida.

The Journal of the American Dental Association published preliminary data suggesting a statistical association between hypodontia of the permanent teeth and epithelial ovarian cancer (EOC). The study shows that women with EOC are 8.1 times more likely to have hypodontia than are women without EOC. The suggestion therefore is that hypodontia can serve as a "marker" for potential risk of EOC in women.

Also the increased frequency of hypodontia in twins and low birth weight in twins with hypodontia suggests that environmental factors during perinatal are responsible hypodontia.

In the 1960s and 1970s, several studies were conducted sponsored by the U.S. Atomic Energy Commission, with the aim of finding a link between genetics and hypodontia.

There is evidence of hereditary factors along with some evidence of environmental factors leading to this condition. While a single excess tooth is relatively common, multiple hyperdontia is rare in people with no other associated diseases or syndromes. Many supernumerary teeth never erupt, but they may delay eruption of nearby teeth or cause other dental or orthodontic problems. Molar-type extra teeth are the rarest form. Dental X-rays are often used to diagnose hyperdontia.

It is suggested that supernumerary teeth develop from a third tooth bud arising from the dental lamina near the regular tooth bud or possibly from splitting the regular tooth bud itself. Supernumerary teeth in deciduous (baby) teeth are less common than in permanent teeth.

Another abnormal condition is hypodontia, in which there are fewer than the usual number of teeth.

Hyperdontia is seen in a number of disorders, including Gardner's syndrome and cleidocranial dysostosis, where multiple supernumerary teeth are seen that are usually impacted.

Supernumerary body parts are most commonly a congenital disorder involving the growth of an additional part of the body and a deviation from the body plan. Body parts may be easily visible or hidden away, such as internal organs.

Many additional body parts form by the same process as conjoined twins: the zygote begins to split but fails to completely separate. This condition may also be a symptom of repeated occurrences of continuous inbreeding in a genetic line.

Specific types of additional body parts include:

- Accessory breast – one or more additional breasts

- Accessory spleen – one or more additional spleens

- Cervical rib – an additional rib

- Diphallia - Having two penes/penises.

- Hermaphroditism – having both sexes' sex organs

- Hyperdontia – additional teeth

- Pelvic digit – a bony growth in the soft tissue of the pelvic region

- Polycephaly – an extra head

- Polydactyly – additional fingers or toes

- Polymelia — an extra arm or leg.

- Polyorchidism – having three or more testicles

- Supernumerary bones – these additional bones are fairly common, particularly in the feet, and are frequently mistaken for fractures on x-rays.

- Supernumerary kidney – a third kidney

- Supernumerary nipples – an additional nipple

- Supernumerary phantom limbs – where the brain acts as though a limb were there, but it is not.

- Syndactyly – webbing between the fingers or toes

- Uterus didelphys – two vaginal canals and/or uteri