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.

Genetic causes also involve the genes MSX1 and PAX9.

Genetic associations for selective tooth agenesis ("STHAG") include:

Prosthetic replacement of missing teeth is possible using dental implant technology or dentures. This treatment can be successful in giving patients with anodontia a more aesthetically pleasing appearance. The use of an implant prosthesis in the lower jaw could be recommended for younger patients as it is shown to significantly improve the craniofacial growth, social development and self-image. The study associated with this evidence worked with individuals who had ectodermal dysplasia of varying age groups of up to 11, 11 to 18 and more than 18 years. It was noted that the risk of implant failure was significantly higher in patients younger than 18 years, but there is significant reason to use this methodology of treatment in those older. Overall the use of an implant-prosthesis has a considerable functional, aesthetic and psychological advantage when compared to a conventional denture, in the patients.

In dentistry, anodontia, also called anodontia vera, is a rare genetic disorder characterized by the congenital absence of all primary or permanent teeth. It is associated with the group of skin and nerve syndromes called the ectodermal dysplasias. Anodontia is usually part of a syndrome and seldom occurs as an isolated entity.

Congenital absence of permanent teeth can present as hypodontia, usually missing 1 or 2 permanent teeth, or oligodontia that is the congenital absence of 6 or more teeth. Congenital absence of all wisdom teeth, or third molars, is relatively common. Anodontia is the congenital absence of teeth and can occur in some or all teeth (partial anodontia or hypodontia), involve two dentitions or only teeth of the permanent dentition (Dorland's 1998). Approximately 1% of the population suffers from oligodontia. Many denominations are attributed to this anomaly: partial anodontia, hypodontia, oligodontia, the congenital absence, anodontia, bilateral aplasia. Anodontia being the term used in controlled vocabulary Medical Subject Headings (MeSH) from MEDLINE which was developed by the United States National Library of Medicine. The congenital absence of at least one permanent tooth is the most common dental anomaly and may contribute to masticator dysfunction, speech impairment, aesthetic problems, and malocclusion (Shapiro and Farrington 1983). Absence of lateral incisors represents a major stereotype. Individuals with this condition are perceived as socially most aggressive compared with people without anodontia (Shaw 1981).

A large number of human gene defects can cause ectrodactyly. The most common mode of inheritance is autosomal dominant with reduced penetrance, while autosomal recessive and X-linked forms occur more rarely. Ectrodactyly can also be caused by a duplication on 10q24. Detailed studies of a number of mouse models for ectrodactyly have also revealed that a failure to maintain median apical ectodermal ridge (AER) signalling can be the main pathogenic mechanism in triggering this abnormality.

A number of factors make the identification of the genetic defects underlying human ectrodactyly a complicated process: the limited number of families linked to each split hand/foot malformation (SHFM) locus, the large number of morphogens involved in limb development, the complex interactions between these morphogens, the involvement of modifier genes, and the presumed involvement of multiple gene or long-range regulatory elements in some cases of ectrodactyly. In the clinical setting these genetic characteristics can become problematic and making predictions of carrier status and severity of the disease impossible to predict.

In 2011, a novel mutation in DLX5 was found to be involved in SHFM.

Ectrodactyly is frequently seen with other congenital anomalies. Syndromes in which ectrodactyly is associated with other abnormalities can occur when two or more genes are affected by a chromosomal rearrangement. Disorders associated with ectrodactyly include Ectrodactyly-Ectodermal Dysplasia-Clefting (EEC) syndrome, which is closely correlated to the ADULT syndrome and Limb-mammary (LMS) syndrome, Ectrodactyly-Cleft Palate (ECP) syndrome, Ectrodactyly-Ectodermal Dysplasia-Macular Dystrophy syndrome, Ectrodactyly-Fibular Aplasia/Hypoplasia (EFA) syndrome, and Ectrodactyly-Polydactyly. More than 50 syndromes and associations involving ectrodactyly are distinguished in the London Dysmorphology Database.

Ectrodactyly can be caused by various changes to 7q. When 7q is altered by a deletion or a translocation ectrodactyly can sometimes be associated with hearing loss. Ectrodactyly, or Split hand/split foot malformation (SHFM) type 1 is the only form of split hand/ malformation associated with sensorineural hearing loss.

Type VII of radial polydactyly is associated with several syndromes:

Holt–Oram syndrome, Fanconi anemia (aplastic anemia by the age of 6), Townes–Brocks syndrome, and Greig cephalopolysyndactyly (also known to occur with ulnar polydactyly).

The syndromes associated with central polydactyly are:

Bardet–Biedl syndrome,

Meckel syndrome,

Pallister–Hall syndrome,

Legius syndrome,

Holt–Oram syndrome,

Also, central polydactyly can be associated with syndactyly and cleft hand.

Other syndromes including polydactyly include acrocallosal syndrome, basal cell nevus syndrome, Biemond syndrome, ectrodactyly-ectodermal dysplasias-cleft lip/palate syndrome, mirror hand deformity, Mohr syndrome, oral-facial-digital syndrome, Rubinstein-Taybi syndrome, short rib polydactyly, and VATER association.

It can also occur with a triphalangeal thumb.

Ectrodactyly–ectodermal dysplasia–cleft syndrome, or EEC, and also referred to as EEC syndrome (also known as "Split hand–split foot–ectodermal dysplasia–cleft syndrome") is a rare form of ectodermal dysplasia, an autosomal dominant disorder inherited as an genetic trait. EEC is characterized by the triad of ectrodactyly, ectodermal dysplasia, and facial clefts. Other features noted in association with EEC include vesicoureteral reflux, recurrent urinary tract infections, obstruction of the nasolacrimal duct, decreased pigmentation of the hair and skin, missing or abnormal teeth, enamel hypoplasia, absent punctae in the lower eyelids, photophobia, occasional cognitive impairment and kidney anomalies, and conductive hearing loss.

Zadik–Barak–Levin syndrome (ZBLS) is a congenital disorder in humans. Presenting conditions include primary hypothyroidism, cleft palate, hypodontia, and ectodermal dysplasia. It is the result of an embryonic defect in the mesodermal-ectodermal midline development.

Larsen syndrome (LS) is a congenital disorder discovered in 1950 by Larsen and associates when they observed dislocation of the large joints and face anomalies in six of their patients. Patients with Larsen syndrome normally present with a variety of symptoms, including congenital anterior dislocation of the knees, dislocation of the hips and elbows, flattened facial appearance, prominent foreheads, and depressed nasal bridges. Larsen syndrome can also cause a variety of cardiovascular and orthopedic abnormalities. This rare disorder is caused by a genetic defect in the gene encoding filamin B, a cytoplasmic protein that is important in regulating the structure and activity of the cytoskeleton. The gene that influences the emergence of Larsen syndrome is found in chromosome region, 3p21.1-14.1, a region containing human type VII collagen gene. Larsen syndrome has recently been described as a mesenchyme disorder that affects the connective tissue of an individual. Autosomal dominant and recessive forms of the disorder have been reported, although most cases are autosomal dominant. Reports have found that in Western societies, Larsen syndrome can be found in one in every 100,000 births, but this is most likely an underestimate because the disorder is frequently unrecognized or misdiagnosed.

Filamins are cytoplasmic proteins that regulate the structure and activity of the cytoskeleton. These proteins serve as scaffolds on which intracellular signaling and protein trafficking are organized. Filamin B has been found to be expressed in human growth plate chondrocytes, which are especially important in vertebrae segmentation and skeleton morphogenesis. Genetic analysis of patients with Larsen syndrome has found the syndrome is caused by missense mutations in the gene that codes for filamin B. These mutations cause an accelerated rate of apoptosis in the epiphyseal growth plates of individuals with the mutation. The defects can cause short stature and other symptoms associated with Larsen syndrome.

Schöpf–Schulz–Passarge syndrome (also known as "eyelid cysts, palmoplantar keratoderma, hypodontia, and hypotrichosis") is an autosomal recessive condition with diffuse symmetric palmoplantar keratoderma, with the palmoplantar keratoderma and fragility of the nails beginning around age 12. In addition to palmoplantar keratoderma, other symptoms include hypodontia, hypotrichosis, nail dystrophies, and eyelid cysts (apocrine hidrocystomas). Patients may also develop syringofibroadenoma and squamous cell carcinomas.

It was characterized in 1971.

It has been associated with WNT10A.

Lelis syndrome it is a genetic disorder, a rare condition with dermatological and dental findings characterized by the association of ectodermal dysplasia (hypotrichosis and hypohidrosis) with acanthosis nigricans. Other clinical features may include palmoplantar hyperkeratosis, nail dystrophy, intellectual deficit, disturbances of skin pigmentation (perioral and periorbital hyperpigmentation, vitiligo, and perinevic leukoderma) and hypodontia. Transmission is autosomal recessive.

Ectrodactyly involves the deficiency or absence of one or more central digits of the hand or foot and is also known as split hand–split foot malformation (SHFM). The hands and feet of people with ectrodactyly are often described as "claw-like" and may include only the thumb and one finger (usually either the little finger, ring finger, or a syndactyly of the two) with similar abnormalities of the feet.

Ectodermal dysplasia describes abnormalities of structures derived from the embryonic ectoderm. These abnormalities affect both the superficial ectodermal layer, as well as the mesectodermal layer constituted by the neural crest.

Tooth and nail syndrome (also known as "Hypodontia with nail dysgenesis," and "Witkop syndrome") is a rare disorder, first described in 1965, characterized by nails that are thin, small, and friable, and which may show koilonychia at birth.

It is associated with "MSX1".

Oligodactyly (from the Ancient Greek "oligos" meaning "few" and δάκτυλος "daktylos" meaning "finger") is the presence of fewer than five fingers or toes on a hand or foot.

It is quite often incorrectly called "hypodactyly", but the Greek prefixes and are used for scales (e.g. in hypoglycaemia and hypercholesterolemia). This as opposed to or scales, where and should be used (e.g. in oligarchy and polygamy). Oligodactyly is therefore the opposite of polydactyly. Very rare, this medical condition usually has a genetic or familial cause.

Oligodactyly is sometimes a sign or symptom of several syndromes including Poland syndrome and Weyer Ulnar Ray Syndrome. It is a type of Dysmelia.

Ectrodactyly is an extreme instance of oligodactyly, involving the absence of one or more central digits of the hand or foot and is also known as split hand/split foot malformation (SHFM). The hands and feet of people with ectrodactyly are often described as "claw-like" and may include only the thumb and one finger (usually either the little finger, ring finger, or a syndactyly of the two) with similar abnormalities of the feet.

People with oligodactyly often have full use of the remaining digits and adapt well to their condition. They are not greatly hindered in their daily activities, if at all. Even those with the most extreme forms are known to engage in tasks that require fine control, such as writing and bootmaking as well as working as a cab driver.

Vadoma people of Zimbabwe have a high frequency of oligodactyly.

Heart-hand syndromes are a group of rare diseases that manifest with both heart and limb deformities.

, known heart-hand syndromes include Holt–Oram syndrome, Berk–Tabatznik syndrome, heart-hand syndrome type 3, brachydactyly-long thumb syndrome, patent ductus arteriosus-bicuspid aortic valve syndrome and heart hand syndrome, Slovenian type.

Heart-hand syndrome type 2 is also known as Berk–Tabatznik syndrome. Berk–Tabatznik syndrome is a condition with an unknown cause that shows symptoms of short stature, congenital optic atrophy and brachytelephalangy. This condition is extremely rare with only two cases being found.

Orofaciodigital syndrome 1 (OFD1), also called Papillon-League and Psaume syndrome, is an X-linked congenital disorder characterized by malformations of the face, oral cavity, and digits with polycystic kidney disease and variable involvement of the central nervous system.

Median nail dystrophy (also known as "Dystrophia unguis mediana canaliformis," "Median canaliform dystrophy of Heller," and "Solenonychia") consists of longitudinal splitting or canal formation in the midline of the nail, a split which often resembles a fir tree, occurring at the cuticle and proceeding outward as the nail grows.

Thumbs, which are the most commonly involved, usually show an enlarged lunula resulting probably from repeated pressure applied on the base of the nail.

Recent findings in genetic research have suggested that a large number of genetic disorders, both genetic syndromes and genetic diseases, that were not previously identified in the medical literature as related, may be, in fact, highly related in the genotypical root cause of these widely varying, phenotypically-observed disorders. Orofaciodigital syndrome has been found to be a ciliopathy. Other known ciliopathies include primary ciliary dyskinesia, Bardet-Biedl syndrome, polycystic kidney disease and polycystic liver disease, nephronophthisis, Alstrom syndrome, Meckel-Gruber syndrome and some forms of retinal degeneration.

TBS is an autosomal dominant involving the a mutation of the gene SALL1, which encodes a transcriptional repressor which interacts with TRF1/PIN2 and localizes to pericentromeric heterochromatin. The clinical features of TBS overlap with VATER and VACTERL associations, oculo-auriculo-vertebral (OAV) spectrum, branchio-oto-renal (BOR) syndrome, and Fanconi anemia and other 'anus-hand-ear' syndromes.

Although some symptoms can be life-threatening, many people diagnosed with Townes-Brocks Syndrome live a normal lifespan.

Townes–Brocks syndrome (TBS) is a rare genetic disease that has been described in approximately 200 cases in the published literature. It affects both males and females equally. The condition was first identified in 1972. by Philip L. Townes, MD, PhD, who was at the time a human geneticists and Professor of Pediatrics, and Eric Brocks, MD, who was at the time a medical student, both at the University of Rochester.

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.