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

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.

Wearing shoes to protect barefoot trauma has shown decrease in incidence in ainhum. Congenital pseudoainhum cannot be prevented and can lead to serious birth defects.

Minor degrees of curvature are common. Reports of incidence vary between 1% and 19.5%.

Hand-foot-genital syndrome is inherited in an autosomal dominant manner. The proportion of cases caused by de novo mutations is unknown because of the small number of individuals described. If a parent of the proband is affected, the risk to the siblings is 50%. When the parents are clinically unaffected, the risk to the sibs of a proband appears to be low. Each child of an individual with HFGS has a 50% chance of inheriting the mutation. Prenatal testing may be available through laboratories offering custom prenatal testing for families in which the disease-causing mutation has been identified in an affected family member.

Clinodactyly is an autosomal dominant trait that has variable expressiveness and incomplete penetrance.

Clinodactyly can be passed through inheritance and presents as either an isolated anomaly or a component manifestation of a genetic syndrome. Many syndromes are associated with clinodactyly, including Down Syndrome, Turner syndrome, Aarskog syndrome, Carpenter syndrome, Seckel syndrome, Cornelia de Lange syndrome, orofaciodigital syndrome 1, 13q deletion syndrome, XXYY syndrome and Silver–Russell syndrome.

When identified prenatally, for example during obstetric ultrasonography, it may be an indication for intrauterine sampling for fetal chromosome analysis as it is statistically correlated with increased risk of chromosome aberration in the fetus.

Ainhum is an acquired and progressive condition, and thus differs from congenital annular constrictions. Ainhum has been much confused with similar constrictions caused by other diseases such as leprosy, diabetic gangrene, syringomyelia, scleroderma or Vohwinkel syndrome. In this case, it is called pseudo-ainhum, treatable with minor surgery or intralesional corticosteroids, as with ainhum. It has even been seen in psoriasis or it is acquired by the wrapping toes, penis or nipple with hairs, threads or fibers. Oral retinoids, such as tretinoin, and antifibrotic agents like tranilast have been tested for pseudo-ainhum. Impending amputation in Vohwinkel syndrome can sometimes be aborted by therapy with oral etretinate. It is rarely seen in the United States but often discussed in the international medical literature.

Severe congenital onychogryphosis affecting all twenty nailbeds has been recorded in two families who exhibit the dominant allele for a certain gene. Congenital onychogryphosis of the fifth toe (the little toe) is fairly common, but asymptomatic and seldom brought to the attention of medical professionals. Rather, it is brought to the attention of manicurists who routinely file the clawed toenail flat.

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.

Some recommend avulsion of the nail plate with surgical destruction of the nail matrix with phenol or the carbon dioxide laser, if the blood supply is good.

Diagnosis is based on physical examination including radiographs of the hands and feet and imaging studies of the kidneys, bladder, and female reproductive tract. HOXA13 is the only gene known to be associated with HFGS. Approximately 60% of mutations are polyalanine expansions. Molecular genetic testing is clinically available.

The accessory nail of the fifth toe is a physical trait of the small toe, where a minuscule "sixth toenail" is present in the outer corner of the nail situated on the smallest toe. It is commonly perceived to be especially prevalent amongst Han Chinese;.

Coffin–Siris Syndrome is a rare genetic disorder that causes developmental delays and absent fifth finger and toe nails.

There had been 31 reported cases by 1991. The numbers of occurrence since then has grown and is reported to be around 80.

The differential includes Nicolaides–Baraitser syndrome.

Some individuals have preaxial polydactyly in the feet (unilateral in one, bilateral in 13), consisting of a small extra biphalangeal toe, in most cases with an associated rudimentary extra metatarsal, lying in a soft tissue web between the hallux and second toe. In some cases, this was accompanied by hypoplasia of the head of the first metatarsal and absence of both phalanges of the hallux.

The trait can be observed on either one or both feet, where there is a separation of the toenail situated on the smallest toe. The separated part of the nail forms a smaller "sixth toenail" on the corner of the larger, or "main" section of the toenail, on the outermost side of the foot, which protrudes outwards from the corner of the larger nail. The additional "nail" can be cut with a nail clipper, just like any other nail.

Autosomal recessive inheritance is the most likely, but sporadic mutations and autosomal dominant cases may also occur.

This syndrome has been associated with mutations in the ARID1B gene.

Mutations in SOX11 are associated to this syndrome.

The diagnosis is generally based on the presence of major and at least one minor clinical sign and can be confirmed by molecular genetic testing of the causative genes. Recent studies revealed that fifth finger nail/distal phalanx hypoplasia or aplasia is not a mandatory finding.

Training of the feet, utilizing foot gymnastics and going barefoot on varying terrain, can facilitate the formation of arches during childhood, with a developed arch occurring for most by the age of four to six years. Ligament laxity is also among the factors known to be associated with flat feet. One medical study in India with a large sample size of children who had grown up wearing shoes and others going barefoot found that the longitudinal arches of the bare-footers were generally strongest and highest as a group, and that flat feet were less common in children who had grown up wearing sandals or slippers than among those who had worn closed-toe shoes. Focusing on the influence of footwear on the prevalence of pes planus, the cross-sectional study performed on children noted that wearing shoes throughout early childhood can be detrimental to the development of a normal or a high medial longitudinal arch. The vulnerability for flat foot among shoe-wearing children increases if the child has an associated ligament laxity condition. The results of the study suggest that children be encouraged to play barefooted on various surfaces of terrain and that slippers and sandals are less harmful compared to closed-toe shoes. It appeared that closed-toe shoes greatly inhibited the development of the arch of the foot more so than slippers or sandals. This conclusion may be a result of the notion that intrinsic muscle activity of the arch is required to prevent slippers and sandals from falling off the child’s foot.

Morton's Toe is a minority variant of foot shape. Its recorded prevalence varies in different populations, with estimates from 2.95% to 22%.

Malalignment of the nail plate is a congenital malalignment of the nail of the great toe, and is often misdiagnosed although it is a common condition.

Diplopodia is a congenital anomaly in tetrapods that involves duplication of elements of the foot on the hind limb. It comes from the Greek roots diplo = "double" and pod = "foot". Diplopodia is often found in conjunction with other structural abnormalities and can be lethal. It is more extreme than polydactyly, the presence of extra digits.

Flat feet can also develop as an adult ("adult acquired flatfoot") due to injury, illness, unusual or prolonged stress to the foot, faulty biomechanics, or as part of the normal aging process. This is most common in women over 40 years of age. Known risk factors include obesity, hypertension and diabetes. Flat feet can also occur in pregnant women as a result of temporary changes, due to increased elastin (elasticity) during pregnancy. However, if developed by adulthood, flat feet generally remain flat permanently.

If a youth or adult appears flatfooted while standing in a full weight bearing position, but an arch appears when the person plantarflexes, or pulls the toes back with the rest of the foot flat on the floor, this condition is called flexible flatfoot. This is not a true collapsed arch, as the medial longitudinal arch is still present and the windlass mechanism still operates; this presentation is actually due to excessive pronation of the foot (rolling inwards), although the term 'flat foot' is still applicable as it is a somewhat generic term. Muscular training of the feet is helpful and will often result in increased arch height regardless of age.

There is still some discussion on whether FND is sporadic or genetic. The majority of FND cases are sporadic. Yet, some studies describe families with multiple members with FND. Gene mutations are likely to play an important role in the cause. Unfortunately, the genetic cause for most types of FND remains undetermined.

There are many hypotheses about how clubfoot develops. Some hypothesis include: environmental factors, genetics, or a combination of both. Research has not yet pinpointed the root cause, but many findings agree that "it is likely there is more than one different cause and at least in some cases the phenotype may occur as a result of a threshold effect of different factors acting together."

Some researchers hypothesize, from the early development stages of humans, that clubfoot is formed by a malfunction during gestation. Early amniocentesis (11–13 wks) is believed to increase the rate of clubfoot because there is an increase in potential amniotic leakage from the procedure. Underdevelopment of the bones and muscles of the embryonic foot may be another underlying cause. In the early 1900s it was thought that constriction of the foot by the uterus contributed to the occurrence of clubfoot.

Underdevelopment of the bones also affects the muscles and tissues of the foot. Abnormality in the connective tissue causes "the presence of increased fibrous tissue in muscles, fascia, ligaments and tendon sheaths".

There are few good estimates of prevalence for pes cavus in the general community. While pes cavus has been reported in between 2 and 29% of the adult population, there are several limitations of the prevalence data reported in these studies. Population-based studies suggest the prevalence of the cavus foot is approximately 10%.

The most common digit to become ingrown is the big toe, but ingrowth can occur on any nail. Ingrown nails can be avoided by cutting nails straight across; not along a curve, not too short and no shorter than the flesh around it. Footwear that is too small or too narrow, or with too shallow of a "toe box", will exacerbate any underlying problem with a toenail. Sharp square corners may be uncomfortable and cause snagging on socks. Proper cutting leaves the leading edge of the nail free of the flesh, precluding it from growing into the toe. Filing of the corner is reasonable. Some nails require cutting of the corners far back to remove edges that dig into the flesh; this is often done as a partial wedge resection by a podiatrist. Ingrown toe nails can be caused by injury, commonly blunt trauma in which the flesh is pressed against the nail causing a small cut that swells. Injury to the nail can cause it to grow abnormally, making it wider or thicker than normal, or even bulged or crooked.