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.

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

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.

The cause of fibular hemimelia is unclear. Purportedly, there have been some incidents of genetic distribution in a family; however, this does not account for all cases. Maternal viral infections, embryonic trauma, teratogenic environmental exposures or vascular dysgenesis (failure of the embryo to form a satisfactory blood supply) between four and seven weeks gestation are considered possible causes.

In an experimental mouse model, change in the expression of a homeobox gene led to similar, but bilateral, fibular defects.

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.

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.

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.

Fibular hemimelia or longitudinal fibular deficiency is "the congenital absence of the fibula and it is the most common congenital absence of long bone of the extremities." It is the shortening of the fibula at birth, or the complete lack thereof. In humans, the disorder can be noted by ultrasound in utero to prepare for amputation after birth or complex bone lengthening surgery. The amputation usually takes place at six months with removal of portions of the legs to prepare them for prosthetic use. The other treatments which include repeated corrective osteotomies and leg-lengthening surgery (Ilizarov apparatus) are costly and associated with residual deformity.

The histological and ultrastructural features of Ledderhose and Dupuytren's disease are the same, which supports the hypothesis that they have a common cause and pathogenesis. As with Dupuytren's disease, the root cause(s) of Ledderhose's disease are not yet understood. It has been noted that it is an inherited disease and of variable occurrence within families, i.e. the genes necessary for it may remain dormant for a generation or more and then surface in an individual, or be present in multiple individuals in the same generation with varying degree.

There are certain identified risk factors. The disease is more commonly associated with -

- A family history of the disease

- Higher incidence in males

- Palmar fibromatosis 10-65% of the time.

- Peyronie's disease

- Epilepsy patients

- Patients of diabetes mellitus

There is also a suspected, although unproven, link between incidence and alcoholism, smoking, liver diseases, thyroid problems, and stressful work involving the feet.

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.

Rocker bottom foot, also known as congenital vertical talus, is an anomaly of the foot. It is characterized by a prominent calcaneus (heel bone) and a convex rounded bottom of the foot. It gets its name from the foot's resemblance to the bottom of a rocking chair.

It can be associated with Edwards' syndrome (trisomy 18), Patau syndrome (trisomy 13), Trisomy 9 and mutation in the gene HOXD10.

It can also be associated with Charcots foot.

Congenital causes include:

- Klippel Trenaunay Weber syndrome

- Maffucci syndrome

- macrodystrophia lipomatosa

- neurofibromatosis,

- lipoatrophic diabetes.

- Proteus syndrome, which by one theory accounts for the deformities of the Elephant Man

Type II should be managed conservatively whereas type I and Ia requires to be treated surgically. Surgery involves four major steps:

- Development of the calcaneal part of the foot

- Repositioning of the navicular bone

- New adjustment of the ankle, and

- Various stabilization measures including the Grice operation and transposition of various tendons.

A foot deformity is a disorder of the foot that can be congenital or acquired.

Such deformities can include hammer toe, club foot, flat feet, pes cavus, etc.

There are a number of acquired causes of local gigantism. A body part can attain bigger size from causes as common as the following:

- inflammation, due to trauma or infection

- tumors like osteoid osteoma, melorheostosis, and lipofibromatous hamartoma

- Arteriovenous malformations occurring on a limb, before the closure of epiphyses in long bones

- Elephantiasis, which is quite common in south-east asia due to prevalence of filariasis.

- Still's disease

- amyloidosis

- acromegaly

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".

CHILD syndrome is not fatal unless there are problems with the internal organs. The most common causes of early death in people with the syndrome are cardiovascular malformations. However, central nervous system, skeletal, kidney, lung, and other visceral defects also contribute significantly.

CHILD syndrome occurs almost exclusively in females. Only 2 known cases have been reported in males, one having a normal 46,XY karyotype, suggesting an early postzygotic somatic mutation.

Clubfoot is a birth defect where one or both feet are rotated inwards and downwards. The affected foot, calf, and leg may be smaller than the other. In about half of those affected, both feet are involved. Most cases are not associated with other problems. Without treatment, people walk on the sides of their feet which causes issues with walking.

The exact cause is usually unclear. A few cases are associated with distal arthrogryposis or myelomeningocele. If one identical twin is affected there is a 33% chance the other one will be as well. Diagnosis may occur at birth or before birth during an ultrasound exam.

Initial treatment is most often with the Ponseti method. This involves moving the foot into an improved position followed by casting, which is repeated at weekly intervals. Once the inward bending is improved, the Achilles tendon is often cut and braces are worn until the age of four. Initially the brace is worn nearly continuously and then just at night. In about 20% of cases further surgery is required.

Clubfoot occurs in about one in 1,000 newborns. The condition is less common among the Chinese and more common among Maori. Males are affected about twice as often as females. Treatment can be carried out by a range of healthcare providers and can generally be achieved in the developing world with few resources.

Radioulnar synostosis is one of the more common failures of separation of parts of the upper limb. There are two general types: one is characterized by fusion of the radius and ulna at their proximal borders and the other is fused distal to the proximal radial epiphysis. Most cases are sporadic, congenital (due to a defect in longitudinal segmentation at the 7th week of development) and less often post-traumatic, bilateral in 60%, and more common in males. Familial cases in association with autosomal dominant transmission appear to be concentrated in certain geographic regions, such as Sicily.

The condition frequently is not noted until late childhood, as function may be normal, especially in unilateral cases. Increased wrist motion may compensate for the absent forearm motion. It has been suggested that individuals whose forearms are fixed in greater amounts of pronation (over 60 degrees) face more problems with function than those with around 20 degrees of fixation. Pain is generally not a problem, unless radial head dislocation should occur.

Most examples of radioulnar synostosis are isolated (non-syndromic). Syndromes that may be accompanied by radioulnar synostosis include X chromosome polyploidy (e.g., XXXY) and other chromosome disorders (e.g., 4p- syndrome, Williams syndrome), acrofacial dysostosis, Antley–Bixler syndrome, genitopatellar syndrome, Greig cephalopolysyndactyly syndrome, hereditary multiple osteochondromas (hereditary multiple exostoses), limb-body wall complex, and Nievergelt syndrome.

Craniosynostosis (from cranio, cranium; + syn, together; + ostosis relating to bone) is a condition in which one or more of the fibrous sutures in an infant skull prematurely fuses by turning into bone (ossification). Craniosynostosis has following kinds: scaphocephaly, trigonocephaly, plagiocephaly, anterior plagiocephaly, posterior plagiocephaly, brachycephaly, oxycephaly, pansynostosis.

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.

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.

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 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%.