The exact cause of the condition is unknown. In some cases, close family members may share this condition. In other cases, no other related persons have this condition. The scientific name for the condition is syndactyly, although this term covers both webbed fingers and webbed toes. Syndactyly occurs when apoptosis or programmed cell death during gestation is absent or incomplete. Webbed toes occur most commonly in the following circumstances:

- Syndactyly or Familial Syndactyly

- Down syndrome

It is also associated with a number of rare conditions, notably:

- Aarskog–Scott syndrome

- Acrocallosal syndrome

- Apert's syndrome

- Bardet-Biedl syndrome

- Carpenter syndrome

- Cornelia de Lange syndrome

- Edwards syndrome

- Jackson–Weiss syndrome

- Fetal hydantoin syndrome

- Miller syndrome

- Pfeiffer syndrome

- Smith-Lemli-Opitz syndrome

- Timothy syndrome

- Ectodermal Dysplasia

- Klippel-Feil Syndrome

Omphalocele has been described in two patients with Apert syndrome by Herman T.E. et al. (USA, 2010) and by Ercoli G. et al. (Argentina, 2014). An omphalocele is a birth defect in which an intestine or other abdominal organs are outside of the body of an infant because of a hole in the bellybutton area. However, the association between omphalocele and Apert syndrome is not confirmed yet, so additional studies are necessary.

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.

Surgery is needed to prevent the closing of the coronal sutures from damaging brain development. In particular, surgeries for the LeFort III or monobloc midface distraction osteogenesis which detaches the midface or the entire upper face, respectively, from the rest of the skull, are performed in order to reposition them in the correct plane. These surgeries are performed by both plastic and oral and maxillofacial (OMS) surgeons, often in collaboration.

Triphalangeal thumb can occur in syndromes but it can also be isolated. The triphalangeal thumb can appear in combination with other malformations or syndromes.

Syndromes include:

- Holt-Oram syndrome

- Aase syndrome

- Blackfan-Diamond syndrome

- Townes-Brocks syndrome

Malformations include:

- Radial polydactyly

- Syndactyly

- Claw-like hand or foot

Malformations of the upper extremities can occur In the third to seventh embryonic week. In some cases the TPT is hereditary. In these cases, there is a mutation on chromosome 7q36. If the TPT is hereditary, it is mostly inherited as an autosomal dominant trait, non-opposable and bilateral. The sporadic cases are mostly opposable and unilateral.

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.

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.

Children with Pfeiffer syndrome types 2 and 3 "have a higher risk for neurodevelopmental disorders and a reduced life expectancy" than children with Pfeiffer syndrome type 1, but if treated, favorable outcomes are possible. In severe cases, respiratory and neurological complications often lead to early death.

Webbed toes in humans are a purely cosmetic condition. This condition does not impair the ability to perform any activity, including walking, running, or swimming. Depending on the severity and structure of the webbing, there can be some minor consequences.

People with more severe webbed toes may have a slight disadvantage for activities that benefit from prehensile toes, due to the toes being unable to split or move laterally. Although not scientifically proven, some believe that this condition can possibly allow for a slight advantage, specifically, in athletics. Considering your big toe is a main source for balance, having your second and third toe webbed could virtually be seen as having two big toes. Thus, allowing for better balance in athletics such as running or dance.

Psychological stress may arise from the fear of negative reactions to this condition from people who do not have webbed toes, particularly in severe cases where the nails are stuck visibly close together. Many people with webbed toes can physically feel the toes touching under the fused skin, which can cause psychological discomfort. This is due to the nerves of each toe fully developing and independent muscles working. In other cases where the toes are partially webbed, the webbing holds the separate tips of the toes against one another and prevents the muscles from spreading the toes apart, causing the toes and sometimes nails to press together.

However a disadvantage would be a difficulty in wearing flip-flops or other such footwear in warm countries. People with webbed toes may be unable to wear Toe socks or Vibram FiveFingers shoes. Difficulty navigating rough terrain barefoot, such as rocks at a beach is also common. In some cases the toes grow at different lengths causing the toes to buckle or bend and many people with severe webbed toes experience cramping in these toes due to the muscles and ligaments being strained.

SCS is the most common craniosynostosis syndrome and affects 1 in every 25,000 to 50,000 individuals. It occurs in all racial and ethnic groups, and affects males and females equally. If a parent carries a copy of the SCS gene mutation, then there is a 50% chance their child will also carry a copy of the gene mutation, in which case, the child may or may not show signs of SCS. There is also a 50% chance their child will have two working copies of the gene, and would therefore, not have SCS. If both parents carry a single copy of the SCS gene mutation, then there is a 25% chance their child will have two gene mutation copies (so child would develop severe SCS), a 25% chance their child would have two normal copies of the gene (so would be completely normal), and a 50% chance their child would carry one gene mutation copy and 1 normal copy (so child may or may not display SCS). In rare situations, two normal parents can have a child with SCS due to a "de novo" mutation. The exact cause of the "de novo" mutation is unknown, but it doesn't seem to be related to anything that the parents did or didn't do during the pregnancy. SCS due to a "de novo" mutation is so rare that the proportion of past cases is unknown.

YVS has been described relatively recently in the 1980s and since then less than 15 cases have been reported around the world. Many of the infants did not survive beyond one year of age.

According to the National Human Genome Research Institute, Poland syndrome affects males three times as often as females and affects the right side of the body twice as often as the left. The incidence is estimated to range from one in 7,000 to one in 100,000 live births.

Synpolydactyly is a joint presentation of syndactyly (fusion of digits) and polydactyly (production of supernumerary digits). This is often a result of a mutation in the HOX D13 gene.

Types include:

Three main support groups of this syndrome are the ASGA in Australia, The Association for Children with Genetic Disorders in Poland, and the Association of People of Genetic Disorders in Greece.

The cause of Poland syndrome is unknown. However, an interruption of the embryonic blood supply to the arteries that lie under the collarbone (subclavian arteries) at about the 46th day of embryonic development is the prevailing theory.

The subclavian arteries normally supply blood to embryonic tissues that give rise to the chest wall and hand. Variations in the site and extent of the disruption may explain the range of signs and symptoms that occur in Poland syndrome. Abnormality of an embryonic structure called the apical ectodermal ridge, which helps direct early limb development, may also be involved in this disorder.

The actual incidence of this disease is not known, but only 243 cases have been reported in the scientific literature, suggesting an incidence of on the order of one affected person in ten million people.

The key problem is the early fusion of the skull, which can be corrected by a series of surgical procedures, often within the first three months after birth. Later surgeries are necessary to correct respiratory and facial deformities.

Acrocephalosyndactylia (or acrocephalosyndactyly) is the common presentation of craniosynostosis and syndactyly.

It has several different types:

- type 1 - Apert syndrome

- type 2 - Crouzon syndrome

- type 3 - Saethre-Chotzen syndrome

- type 5 - Pfeiffer syndrome

A related term, "acrocephalopolysyndactyly" (ACPS), refers to the inclusion of polydactyly to the presentation. It also has multiple types:

- type 1 - Noack syndrome; now classified with Pfeiffer syndrome

- type 2 - Carpenter syndrome

- type 3 - Sakati-Nyhan-Tisdale syndrome

- type 4 - Goodman syndrome; now classified with Carpenter syndrome

- type 5 - Pfeiffer syndrome

It has been suggested that the distinction between "acrocephalosyndactyly" versus "acrocephalopolysyndactyly" should be abandoned.

Polysyndactyly is an hereditary anatomical malformation combining polydactyly and syndactyly. There is also a type called "crossed" polysyndactyly

Prenatal diagnosis of Saethre-Chotzen Syndrome in high risk pregnancies is doable, but very uncommon and rarely performed. Furthermore, this is only possible if the mutation causing the disease has already been identified within the family genome. There are a few different techniques in which prenatal testing can be carried out. Prenatal testing is usually performed around 15–18 weeks, using amniocentesis to extract DNA from the fetus's cells. Prenatal testing can also be performed during weeks 10-12 using chorionic villus sampling (CVS) to extract DNA from the fetus. Recently, there has been an increased interest in utilizing ultrasound equipment in order to detect fetal skull abnormalities due to immature fusion of the cranial sutures.

Five types of syndactyly have been identified in humans. The corresponding loci associated with these types and their common phenotypical expression are as follows:

- "type I": 2q34-q36; webbing occurs between middle and ring fingers and/or second and third toes.

- "type II": 2q31; also involves long and ring fingers, but has a sixth finger merged in between.

- "type III": 6q21-q23; small finger is merged into the ring finger.

- "type IV": 7q36; involves all fingers and/or toes.

- "type V": 2q31-q32; similar to type I, but the metacarpals and metatarsals may also be fused.

It is likely that this syndrome is inherited in an autosomal dominant fashion, however there may be a recessive form with hypotonia and developmental delay.