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.

Blount's disease occurs in young children and adolescents. The cause is unknown but is thought to be due to the effects of weight on the growth plate. The inner part of the tibia, just below the knee, fails to develop normally, causing angulation of the bone.

Unlike bowlegs, which tend to straighten as the child develops, Blount's disease is progressive and the condition worsens. It can cause severe bowing of the legs and can affect one or both legs.

This condition is more common among children of African ancestry. It is also associated with obesity, short stature, and early walking. There does not appear to be an obvious genetic factor.

The cause of PFFD is uncertain. Two hypotheses have been advanced. The theory of sclerotome subtraction posits injury to neural crest cells that are the precursors to sensory nerves at the level of L4 and L5. Histologic studies of a fetus with unilateral PFFD have prompted an alternative hypothesis that PFFD is caused by a defect in maturation of chondrocytes (cartilage cells) at the growth plate. In either hypothesis, the agent causing the injury is usually not known. Thalidomide is known to cause PFFD when the mother is exposed to it in the fifth or sixth week of pregnancy, and it is speculated that exposure to other toxins during pregnancy may also be a cause. Other etiologies that have been suggested, but not proven, include anoxia, ischemia, radiation, infection, hormones, and mechanical force. PFFD occurs sporadically, and does not appear to be hereditary.

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 exact cause of congenital amputation is unknown and can result from a number of causes. However, most cases show that the first three months in a pregnancy are when most birth defects occur because that is when the organs of the fetus are beginning to form. One common cause is amniotic band syndrome, which occurs when the inner fetal membrane (amnion) ruptures without injury to the outer membrane (chorion). Fibrous bands from the ruptured amnion float in the amniotic fluid and can get entangled with the fetus, thus reducing blood supply to the developing limbs to such an extent that the limbs can become strangulated; the tissues die and are absorbed into the amniotic fluid. A baby with congenital amputation can be missing a portion of a limb or the entire limb, which results in the complete absence of a limb beyond a certain point where only a stump is left is known as transverse deficiency or amelia. When a specific part is missing, it is referred to as longitudinal deficiency. Finally, phocomelia occurs when only a mid-portion of a limb is missing; for example when the hands or feet are directly attached to the trunk of the body.

Amnion ruptures can be caused by:

- teratogenic drugs (e.g. thalidomide, which causes phocomelia), or environmental chemicals

- ionizing radiation (atomic weapons, radioiodine, radiation therapy)

- infections

- metabolic imbalance

- trauma

Congenital amputation is the least common reason for amputation, but it is projected that one in 2000 babies are born each year with a missing or deformed limb. During certain periods in history, an increase in congenital amputations has been documented. One example includes the thalidomide tragedy that occurred in the 1960s when pregnant mothers were given a tranquilizer that contained the harmful drug, which produced an increase in children born without limbs. Another example was the 1986 Chernobyl catastrophe in Ukraine, where the radiation exposure caused many children to be born with abnormal or missing limbs .

It can result from syphilis, yaws, Paget's disease of bone, Vitamin D deficiency, or Weismann-Netter-Stuhl syndrome.

It can be due to osteomalacia

The incidence is less than 1/1.000.000. Fewer than 50 cases have been reported so far.

At the core of the disorder there is a homozygous or compound heterozygous mutation or deletion of the SHOX (Short Stature Homeobox), SHOXY (Short Stature Homeobox Y-linked) or PAR1 (where SHOX enhancer elements are located) genes, which is inherited in a pseudosomal recessive manner.

There are typically four classes (or "types") of PFFD, ranging from class A to class D, as detailed by Aitken.

Hypophalangism is a congenital absence of one or more phalanges (bones of the fingers and toes).

In most cases persisting after childhood, there is little or no effect on the ability to walk. Due to uneven stress and wear on the knees, however, even milder manifestations can see an accelerated onset of arthritis.

It is caused by mutations in the SHOX gene found in the pseudoautosomal region PAR1 of the X and Y chromosomes, at band Xp22.33 or Yp11.32.

SHOX gene deletions have been identified as the major cause of Leri–Weill syndrome.

Leri–Weill dyschondrosteosis is characterized by mesomelic short stature, with bowing of the radius more so than the ulna in the forearms and bowing of the tibia while sparing the fibula.

Studies suggest that prenatal care for mothers during their pregnancies can prevent congenital amputation. Knowing environmental and genetic risks is also important. Heavy exposure to chemicals, smoking, alcohol, poor diet, or engaging in any other teratogenic activities while pregnant can increase the risk of having a child born with a congenital amputation. Folic acid is a multivitamin that has been found to reduce birth defects.

Léri–Weill dyschondrosteosis or LWD is a rare pseudoautosomal dominant genetic disorder which results in dwarfism with short forearms and legs (mesomelic dwarfism) and a bayonet-like deformity of the forearms (Madelung's deformity).

Campomelic dysplasia has a reported incidence of 0.05-0.09 per 10000 live births.

In nearly 95% of the cases, death occurs in the neonatal period due to respiratory distress, generally related to small chest size or insufficient development of the trachea and other upper airway structures.

Among survivors of CMD, the skeletal malformations change over time to include worsening scoliosis or kyphosis resulting in decreased trunk size relative to the limb length. Neurological damage is also often seen including mental retardation and deafness. Even among survivors of the prenatal period, CMD patients have shortened life spans due to lifelong respiratory issues. Those patients with ambiguous genitalia or sex reversal at birth, of course, maintain that state, and are either sterile or have reduced fertility.

Hemimelia comprises

- Fibular hemimelia, Congenital longitudinal deficiency of the fibula or Fibular longitudinal meromelia

- Tibial hemimelia, Congenital longitudenal deficiency of the tibia, Congenital aplasia and dysplasia of the tibia with intact fibula, Congenital longitudinal deficiency of the tibia or Tibial longitudinal meromelia

- Radial Hemimelia, Congenital longitudinal deficiency of the radius, Radial clubhand, Radial longitudinal meromelia or Radial ray agenesis

- Ulnar hemimelia, Congenital longitudinal deficiency of the ulna, Ulnar clubhand or Ulnar longitudinal meromelia

Failure to treat Blount's disease may lead to progressive deformity.Blount's disease may come back after surgery, especially in younger children. Because of the bowing, a leg-length discrepancy may result. This may result in disability if the discrepancy is significant (greater than 1 inch) and is not treated.

Pathology is insertional tendinopathy of the medius and tendons and enlargement of the associated bursa.

Gluteals remain inactive in a seated position. Movements that require muscles become more difficult; stress is put on the spine.

Saber shin is a malformation of the tibia. It presents as a sharp anterior bowing, or convexity, of the tibia.

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.

Some parents of children with MHE have observed autism-like social problems in their children. To explore those observations more deeply, a 2012 study by the Sanford-Burnham Medical Research Institute used a mouse model of MHE to observe cognitive function. The findings indicated that the mutant mice endorsed three autistic characteristics: social impairment, impairments in ultrasonic vocalization, and repetitive behavior.

HME is an autosomal dominant hereditary disorder. This means that a patient with HME has a 50% chance of transmitting this disorder to his or her children. Most individuals with HME have a parent who also has the condition, however, approximately 10% -20% of individuals with HME have the condition as a result of a spontaneous mutation and are thus the first person in their family to be affected.

HME has thus far been linked with mutations in three genes.

- EXT1 which maps to chromosome 8q24.1

- EXT2 which maps to 11p13

- EXT3 which maps to the short arm of Chromosome 19 (though its exact location has yet to be precisely determined)

Mutations in these genes typically lead to the synthesis of a truncated EXT protein which does not function normally. It is known that EXT proteins are important enzymes in the synthesis of heparan sulfate; however the exact mechanism by which altered synthesis of heparan sulfate that could lead to the abnormal bone growth associated with HME is unclear. It is thought that normal chondrocyte proliferation and differentiation may be affected, leading to abnormal bone growth. Since the HME genes are involved in the synthesis of a glycan (heparan sulfate), HME may be considered a congenital disorder of glycosylation according to the new CDG nomenclature suggested in 2009.

For individuals with HME who are considering starting a family, preimplantation genetic testing and prenatal diagnosis are available to determine if their unborn child has inherited the disease. HME has a 96% penetrance, which means that if the affected gene is indeed transmitted to a child, the child will have a 96% of actually manifesting the disease, and 4% chance of having the disease but never manifesting it. It should be noted that the 96% penetrance figure comes from one study. Other studies have observed both incomplete and variable penetrance but without calculating the % penetrance, e.g. In both the aforementioned studies the symptomless individuals carrying the faulty gene were predominantly female, leading to speculation that incomplete penetrance is more likely to be exhibited in females. Indeed, other work has shown that boys/men tend to have worse disease than females, as well as that the number of exostoses in affected members of the same family can vary greatly. It is also possible for females to be severely affected.

Symptoms are more likely to be severe if the mutation is on the "ext1" gene rather than "ext2" or "ext3"; "ext1" is also the most commonly affected gene in patients of this disorder.

The congenital absence of the gluteal muscle was described in 1976, as occurring in a brother and sister with absence of gluteal muscles and with spina bifida occulta. It was thought to be caused by an autosomal recessive gene.

Edgar "et al." (2012) reported the case of a 15-year-old white male with congenital absence of the "gluteus maximus" muscles associated with spina bifida occulta, learning disability, optic nerve hypoplasia, scoliosis, and central nervous system hamartomas.

If gluteal muscles were absent the following actions would not be possible. The "gluteus maximus" extends the thigh at the hip in actions like stair climbing, running or walking. It also abducts the thigh, elevates the trunk and also prevents the trunk of a person from moving forward or backward when the rest of the body is in movement. The "gluteal maximus" also aids in stabilizing the femur and the tibia. The "gluteas minimus" and "medius" are also part of the gluteal muscles. If these muscles were missing, the leg would not be able to abduct or medial rotate the thigh. The body would also not be able to shift weight from one side to the other when one foot is on the ground but not another. Considering this a rare congenital disease with other complications, walking would also not be possible in the list of additional symptoms above.

If a child is sickly, either with rickets or any other ailment that prevents ossification of the bones, or is improperly fed, the bowed condition may persist. Thus the chief cause of this deformity is rickets. Skeletal problems, infection, and tumors can also affect the growth of the leg, sometimes giving rise to a one-sided bow-leggedness. The remaining causes are occupational, especially among jockeys, and from physical trauma, the condition being very likely to supervene after accidents involving the condyles of the femur.

Osteofibrous dysplasia is treated with marginal resection with or without bone grafting, depending on the size of the lesion and the extent of bony involvement. However, due to the high rate of recurrence in skeletally immature individuals, this procedure is usually postponed until skeletal maturity.