Numerous associated abnormalities of other organ systems may be present. This heterogeneity requires comprehensive evaluation of all patients and treatment regimes that can vary from modification of activities to extensive spinal surgeries. Furthermore, it is unclear whether Klippel–Feil syndrome is a unique disease, or if it is one part of a spectrum of congenital spinal deformities. Klippel–Feil syndrome is usually diagnosed after birth.

The most common sign of the disorder is restricted mobility of the neck and upper spine. A short neck and low hairline at the back of the head may occur in some patients.

Associated abnormalities may include:

- scoliosis (side-to-side curvature of the spine), which is abnormal curving of the spine. The spine sometimes appears as a "C" or an "S"

- spina bifida, when the spinal canal and the back bone do not close completely during birth

- anomalies of the kidneys and the ribs

- cleft palate (hole in the roof of the mouth)

- dental problems (late dentition, high-risk of caries, oligo- and hypodontia)

- respiratory problems

- heart malformations

- short stature

- Duane syndrome

- Approximately 35% of patients with Klippel–Feil syndrome will also have a congenital elevation of the scapula known as Sprengel's deformity

The disorder also may be associated with abnormalities of the head and face, skeleton, sex organs, muscles, brain and spinal cord, arms, legs, fingers and heart defects. These heart defects often lead to a shortened life expectancy, the average being 35–45 years of age among males and 40–50 among females. This condition is similar to the heart failure seen in gigantism.

In 2011, a study identifying the occurrence of symptoms of 100 patients was published.

Klippel–Feil syndrome is a rare disease, initially reported in 1884 by Maurice Klippel and André Feil from France, characterized by the congenital fusion of any two of the seven cervical vertebrae.

The syndrome occurs in a heterogeneous group of patients unified only by the presence of a congenital defect in the formation or segmentation of the cervical spine. Klippel-Feil results in limited movement of the neck. Klippel–Feil syndrome is sometimes identified by shortness of the neck, but not all people with this disorder have a visibly shortened neck. Some people with the syndrome have a very low hairline.

In 1919, in his PhD thesis, André Feil suggested another classification of the syndrome encompassing not only deformation of the cervical spine but also deformation of the lumbar and thoracic spine.

Symptoms are related to defects in connective tissue.

- Congenital anterior dislocation of the knees

- Dislocation of hips and shoulders

- Flattened facial appearance

- Prominent forehead

- Depressed nasal bridge

- Club foot

- Cervical kyphosis

These symptoms were found in rare cases of Larsen syndrome.

- Cataracts

- Cleft palate

- Extra bones of wrist

- Malocclusion

- Microdontia and hypodontia

- Complete agenesis of anus

- uterus

- Bifid tongue

Robinow noted the resemblance of affected patients' faces to that of a fetus, using the term "fetal facies" to describe the appearance of a small face and widely spaced eyes. Clinical features also may include a short, upturned nose, a prominent forehead, and a flat nasal bridge. The upper lip may be "tented", exposing dental crowding, "tongue tie", or gum hypertrophy.

Though the eyes do not protrude, abnormalities in the lower eyelid may give that impression. Surgery may be necessary if the eyes cannot close fully. In addition, the ears may be set low on the head or have a deformed pinna.

Patients suffer from dwarfism, short lower arms, small feet, and small hands. Fingers and toes may also be abnormally short and laterally or medially bent. The thumb may be displaced and some patients, notably in Turkey, experience ectrodactyly. All patients often suffer from vertebral segmentation abnormalities. Those with the dominant variant have, at most, a single butterfly vertebra. Those with the recessive form, however, may suffer from hemivertebrae, vertebral fusion, and rib anomalies. Some cases resemble Jarcho-Levin syndrome or spondylocostal dysostosis.

Genital defects characteristically seen in males include a micropenis with a normally developed scrotum and testes. Sometimes, testicles may be undescended, or the patient may suffer from hypospadias. Female genital defects may include a reduced size clitoris and underdeveloped labia minora. Infrequently, the labia majora may also be underdeveloped. Some research has shown that females may experience vaginal atresia or haematocolpos.

The autosomal recessive form of the disorder tends to be much more severe. Examples of differences are summarized in the following table:

Individuals affected by ischiopatellar dysplasia commonly have abnormalities of the patella and pelvic girdle, such as absent or delayed patellar and ischial ossification as well as infra-acetabular axe-cut notches. Patellae are typically absent or small in these individuals, when patellae are present they are small and laterally displaced or dislocated. In addition, abnormalities in other parts of their skeleton and dysmorphic features are common in those affected. Other features that have been identified in patients with ischiopatellar dysplasia include foot anomalies, specifically flat feet (pes planus), syndactylism of the toes, short fourth and fifth toes, and a large gap between the first and second toes, femur anomalies, cleft palate, and craniofacial dysmorphisms.

A musculoskeletal abnormality is a disorder of the musculoskeletal system present at birth.

They can be due to deformity or malformation.

An example is Klippel-Feil syndrome.

Although present at birth, some only become obvious postnatally.

Robinow syndrome is an extremely rare genetic disorder characterized by short-limbed dwarfism, abnormalities in the head, face, and external genitalia, as well as vertebral segmentation. The disorder was first described in 1969 by human geneticist Meinhard Robinow, along with physicians Frederic N. Silverman and Hugo D. Smith, in the "American Journal of Diseases of Children". By 2002, over 100 cases had been documented and introduced into medical literature.

Two forms of the disorder exist, dominant and recessive, of which the former is more common. Patients with the dominant version often suffer moderately from the aforementioned symptoms. Recessive cases, on the other hand, are usually more physically marked, and individuals may exhibit more skeletal abnormalities. The recessive form is particularly frequent in Turkey. However, this can likely be explained by a common ancestor, as these patients' families can be traced to a single town in Eastern Turkey. Clusters of the autosomal recessive form have also been documented in Oman and Czechoslovakia.

The syndrome is also known as Robinow-Silverman-Smith syndrome, Robinow dwarfism, fetal face, fetal face syndrome, fetal facies syndrome, acral dysostosis with facial and genital abnormalities, or mesomelic dwarfism-small genitalia syndrome. The recessive form was previously known as Covesdem syndrome.

Ischiopatellar dysplasia is a rare autosomal dominant disorder characterized by a hypoplasia of the patellae as well as other bone anomalies, especially concerning the pelvis and feet.

Gordon syndrome is an extremely rare disorder that belongs to a group of genetic disorders known as the distal arthrogryposes. These disorders typically involve stiffness and impaired mobility of certain joints of the lower arms and legs (distal extremities) including the knees, elbows, wrists, and/or ankles. These joints tend to be permanently fixed in a bent or flexed position (contractures). Gordon syndrome is characterized by the permanent fixation of several fingers in a flexed position (camptodactyly), abnormal bending inward of the foot (clubfoot or talipes), and, less frequently, incomplete closure of the roof of the mouth (cleft palate). In some cases, additional abnormalities may also be present. The range and severity of symptoms may vary from case to case. Gordon syndrome is inherited as an autosomal dominant trait.

Wildervanck syndrome or cervico-oculo-acoustic syndrome comprises a triad of:

- Duane syndrome

- Klippel-Feil anomaly (fused cervical vertebrae)

- congenital hearing loss

The three most common symptoms of Opitz G/BBB syndrome (both type I & II) are hypertelorism (exceptionally wide-spaced eyes), laryngo-tracheo-esophalgeal defects (including clefts and holes in the palate, larynx, trachea and esophagus) and hypospadias (urinary openings in males not at the tip of the penis) (Meroni, Opitz G/BBB syndrome, 2012). Abnormalities in the larynx, trachea and esophagus can cause significant difficulty breathing and/or swallowing and can result in reoccurring pneumonia and life-threatening situations. Commonly, there may be a gap between the trachea and esophagus, referred to as a laryngeal cleft; which can allow food or fluid to enter the airway and make breathing and eating a difficult task.

Genital abnormalities like a urinary opening under the penis (hypospadias), undescended testes (cryptorchidism), underdeveloped scrotum and a scrotum divided into two lobes (bifid scrotum) can all be commonplace for males with the disease.

Developmental delays of the brain and nervous system are also common in both types I and II of the disease. 50% of people with Opitz G/BBB Syndrome will experience developmental delay and mild intellectual disability. This can impact motor skills, speech and learning capabilities. Some of these instances are likened to autistic spectrum disorders. Close to half of the people with Opitz G/BBB Syndrome also have a cleft lip (hole in the lip opening) and possibly a cleft palate (hole in the roof of the mouth), as well. Less than half of the people diagnosed have heart defects, imperforate anus (obstructed anal opening), and brain defects. Of all the impairments, female carriers of X-linked Type I Opitz G/BBB Syndrome usually only have ocular hypertelorism.

Clinical expressions of PPS are highly variable, but include the following:

- Limb findings: an extensive web running from behind the knee down to the heel (90%), malformed toenails, and webbed toes.

- Facial findings: cleft palate with or without cleft lip (75%), pits in the lower lip (40%), and fibrous bands in the mouth known as syngnathia (25%).

- Genital findings (50%): hypoplasia of the labia majora, malformation of the scrotum, and cryptorchidism.

The symptoms and/or signs of branchio-oto-renal syndrome are consistent with underdeveloped (hypoplastic) or absent kidneys with resultant renal insufficiency or renal failure. Ear anomalies include extra openings in front of the ears, extra pieces of skin in front of the ears (preauricular tags), or further malformation or absence of the outer ear (pinna). Malformation or absence of the middle ear is also possible, individuals can have mild to profound hearing loss. People with BOR may also have cysts or fistulae along the sides of their neck.

Nager acrofacial dysostosis is a genetic congenital anomaly syndrome. Nager syndrome displays several or all of the following characteristics: underdevelopment of the cheek and jaw area, down-sloping of the opening of the eyes, lack or absence of the lower eyelashes, kidney or stomach reflux, hammer toes, shortened soft palate, lack of development of the internal and external ear, possible cleft palate, underdevelopment or absence of the thumb, hearing loss (see hearing loss with craniofacial syndromes) and shortened forearms, as well as poor movement in the elbow, and may be characterized by accessory tragi. Occasionally, affected individuals develop vertebral anomalies such as scoliosis. The inheritance pattern is said to be autosomal but there are arguments as to whether it is autosomal dominant or autosomal recessive. Most cases tend to be sporadic. Nager syndrome is also linked to five other similar syndromes: Miller syndrome, Treacher Collins, Pierre Robin, Genee-Wiedemann, and Franceschetti-Zwahlen-Klein.

The following features are observed with VACTERL association:

- V - Vertebral anomalies

- A - Anorectal malformations

- C - Cardiovascular anomalies

- T - Tracheoesophageal fistula

- E - Esophageal atresia

- R - Renal (Kidney) and/or radial anomalies

- L - Limb defects

Although it was not conclusive whether VACTERL should be defined by at least two or three component defects, it is typically defined by the presence of at least three of the above congenital malformations.

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.

A dysostosis is a disorder of the development of bone, in particular affecting ossification.

Examples include craniofacial dysostosis, Klippel–Feil syndrome, and Rubinstein–Taybi syndrome.

It is one of the two categories of constitutional disorders of bone (the other being osteochondrodysplasia).

When the disorder involves the joint between two bones, the term "synostosis" is often used.

Renal (kidney) defects are seen in approximately 50 percent of patients with VACTERL association. In addition, up to 35 percent of patients with VACTERL association have a single umbilical artery (there are usually two arteries and one vein) which is often associated with additional kidney or urologic problems. Renal abnormalities in VACTERL association can be severe, with incomplete formation of one or both kidneys or urologic abnormalities such as obstruction of outflow of urine from the kidneys or severe reflux (backflow) of urine into the kidneys from the bladder. These problems can cause kidney failure early in life and may require kidney transplant. Many of these problems can be corrected surgically before any damage can occur.

Many of the characteristic facial features (among other) of Jackson–Weiss syndrome result from the premature fusion of the skull bones. The following are some of the more common, such as:

- Preaxial foot polydactyl

- Tarsal synostosis

- Frontal bossing

- Proptosis

Ectodermal dysplasia is characterized by absent sweat glands resulting in dry (hypohydrotic), often scale-like skin, sparse and usually coarse scalp hair that is often blonde, sparse eyebrows and eyelashes, and small brittle nails. In addition, abnormalities of ectodermal derivatives, neuroectodermal derivatives, and mesectodermal derivatives are often found. The ectodermal derivative abnormalities can affect the epidermis including mammary, pituitary and sweat glands, as well as hairs, dental enamel, nails, lens, and the internal ear. Neuroectodermal derivatives that can be affected include sensory placodes, cutaneous pigmental cells, and hair buds. Mesectodermal derivatives affected can include the dermis, hypodermis, dentin, head muscles and conjunctival cells, cervicofacial vascular endothelial cells, and part of the maxillofacial skeleton.

The hypohydrotic symptoms of ectodermal dysplasia described above are evidenced not only in the skin of affected individuals, but also in their phonation and voice production. Because the vocal folds may not be as hydrated as is necessary during the adduction phase of vocal fold vibration (due to lack of lubrication), a complete seal may not be accomplished between the folds and mucosal wave movement may be disrupted. This results in air escapement between the folds and the production of breathy voice, which often accompanies the skin abnormalities of ectodermal dysplasia.

Hemivertebrae are wedge-shaped vertebrae and therefore can cause an angle in the spine (such as kyphosis, scoliosis, and lordosis).

Among the congenital vertebral anomalies, hemivertebrae are the most likely to cause neurologic problems. The most common location is the midthoracic vertebrae, especially the eighth (T8). Neurologic signs result from severe angulation of the spine, narrowing of the spinal canal, instability of the spine, and luxation or fracture of the vertebrae. Signs include rear limb weakness or paralysis, urinary or fecal incontinence, and spinal pain. Most cases of hemivertebrae have no or mild symptoms, so treatment is usually conservative. Severe cases may respond to surgical spinal cord decompression and vertebral stabilization.

Associations

Recognised associations are many and include:

Aicardi syndrome,

cleidocranial dysostosis,

gastroschisis 3,

Gorlin syndrome,

fetal pyelectasis 3,

Jarcho-Levin syndrome,

OEIS complex,

VACTERL association.

The probable cause of hemivertebrae is a lack of blood supply causing part of the vertebrae not to form.

Hemivertebrae in dogs are most common in the tail, resulting in a screw shape.

Gordon syndrome (GS), or distal arthrogryposis type 3, is a rare, autosomal dominant disorder characterized by cleft palate and congenital contractures of the hands and feet.

Nager syndrome is thought to be caused by haploinsufficiency of the spliceosomal factor SF3B4.

Popliteal pterygium syndrome (PPS) is an inherited condition affecting the face, limbs, and genitalia. The syndrome goes by a number of names including the "popliteal web syndrome" and, more inclusively, the "facio-genito-popliteal syndrome". The term PPS was coined by Gorlin "et al.." in 1968 on the basis of the most unusual anomaly, the popliteal pterygium (a web behind the knee).