Electrophysiological evidence of denervation with intact motor and sensory nerve conduction findings must be made by using nerve conduction studies, usually in conjunction with EMG. The presence of polyphasic potentials and fibrillation at rest are characteristic of congenital dSMA.

The following are useful in diagnosis:

- Nerve conduction studies (NCS), to test for denervation

- Electromyography (EMG), also to detect denervation

- X-ray, to look for bone abnormalities

- Magnetic resonance imaging (MRI)

- Skeletal muscle biopsy examination

- Serum creatine kinase (CK) level in blood, usually elevated in affected individuals

- Pulmonary function test

Research on prenatal diagnosis has shown that a diagnosis can be made prenatally in approximately 50% of fetuses presenting arthrogryposis. It could be found during routine ultrasound scanning showing a lack of mobility and abnormal position of the foetus. Nowadays there are more options for visualization of details and structures can be seen well, like the use of 4D ultrasound. In clinic a child can be diagnosed with arthrogryposis with physical examination, confirmed by ultrasound, , or muscle biopsy.

Surgery may be necessary to address the congenital deformities frequently occurring in conjunction with arthrogryposis. Surgery on feet, knees, hips, elbows and wrists may also be useful if more range of motion is needed after therapy has achieved maximum results. In some cases, tendon transfers can improve function. Congenital deformities of the feet, hips and spine may require surgical correction at or about one year of age.

Overall prognosis for children with amyoplasia is good. Intensive therapies throughout developing years include physical therapy, occupational therapy and multiple orthopedic procedures. Most children require therapy for years, but almost 2/3 are eventually able to walk, with or without braces, and attend school.

Congenital dSMA has a relatively stable disease course, with disability mainly attributed to increased contractures rather than loss of muscle strength. Individuals frequently use crutches, knee, ankle, and/or foot orthoses, or wheelchairs. Orthopaedic surgery can be an option for some patients with severely impaired movement. Physical therapy and occupational therapy can help prevent further contractures from occurring, though they do not reverse the effects of preexisting ones. Some literature suggests the use of electrical stimulation or botulinum toxin to halt the progression of contractures.

Many other surgeries are also able to improve function in joints of arthrogryposis patients. These surgeries usually exist out of tendon transfers and skin flap movements, adjusted to the individual.

Fibrochondrogenesis is quite rare. A 1996 study from Spain determined a national minimal prevalence for the disorder at 8 cases out of 1,158,067 live births.

A United Arab Emirates (UAE) University report, from early 2003, evaluated the results of a 5-year study on the occurrence of a broad range of osteochondrodysplasias. Out of 38,048 newborns in Al Ain, over the course of the study period, fibrochondrogenesis was found to be the most common of the recessive forms of osteochondrodysplasia, with a prevalence ratio of 1.05:10,000 births.

While these results represented the most common occurrence within the group studied, they do not dispute the rarity of fibrochondrogenesis. The study also included the high rate of consanguinous marriages as a prevailing factor for these disorders, as well as the extremely low rate of diagnosis-related pregnancy terminations throughout the region.

Amniotic band syndrome is considered an accidental event and it does not appear to be genetic or hereditary, so the likelihood of it occurring in another pregnancy is remote. The cause of amnion tearing is unknown and as such there are no known preventative measures.

Amniotic band syndrome is often difficult to detect before birth as the individual strands are small and hard to see on ultrasound. Often the bands are detected indirectly because of the constrictions and swelling upon limbs, digits, etc. Misdiagnosis is also common, so if there are any signs of amniotic bands, further detailed ultrasound tests should be done to assess the severity. 3D ultrasound and MRI can be used for more detailed and accurate diagnosis of bands and the resulting damage/danger to the fetus.

The fibrocartilaginous effects of fibrochondrogenesis on chondrocytes has shown potential as a means to produce therapeutic cellular biomaterials via tissue engineering and manipulation of stem cells, specifically human embryonic stem cells.

Utilization of these cells as curative cartilage replacement materials on the cellular level has shown promise, with beneficial applications including the repair and healing of damaged knee menisci and synovial joints; temporomandibular joints, and vertebra.

There are four levels (or "types") of malformation. The least severe indicates partial deformation (unilateral) of the sacrum. The second level indicates a bilateral (uniform) deformation. The most severe types involve a total absence of the sacrum.

Depending on the type of sacral agenesis, bowel or urinary bladder deficiencies may be present. A permanent colostomy may be necessary in the case of imperforate anus. Incontinence may also require some type of continence control system (e.g., self-catheterization) be utilized. Occasionally if deformities of the knees, legs or feet would prove unresponsive to corrective action, amputation at the knee may be proposed.

Before more comprehensive medical treatment was available, full amputation of the legs at the hip was often performed. More recently, the 'amputation' (actually a disarticulation because no cutting of the bone is involved) is done at the knee for those who have bent knee positions and webbing between thigh and calf to enable more ease of mobility and better seating. Some children with knee disarticulation use prosthetic legs to walk. Prosthetics for children without substantial hip and trunk control is usually abandoned in favor of faster and easier wheelchair mobility as the child's weight and age increases. Children may 'walk' on their hands and generally are able to climb and move about to accomplish whatever they need and want to accomplish. Children more mildly affected may have normal gait and no need for assistive devices for walking. Others may walk with bracing or crutches.

There is typically no cognitive impairment associated with this disability. Adults with this disability live independently, attend college, and have careers in various fields. In 2012, Spencer West, a man with sacral agenesis and both legs amputated, climbed Mt. Kilimanjaro using only his hands.

The diagnosis of AOS is a clinical diagnosis based on the specific features described above. A system of major and minor criteria was proposed.

The combination of two major criteria would be sufficient for the diagnosis of AOS, while a combination of one major and one minor feature would be suggestive of AOS. Genetic testing can be performed to test for the presence of mutation in one of the known genes, but these so far only account for an estimated 50% of patients with AOS. A definitive diagnosis may therefore not be achieved in all cases.

Spinal arteriovenous malformations (AVMs, or angiomatous malformations) are congenital (from birth) abnormalities of blood vessels. Arteries that directly communicate with veins bypass the capillary network (which has not yet developed) and thus creates a shunt. AVMs appear as a mass of , dilated vessels. In regards to the spinal cord, they are usually located in the thoracolumbar region (between the thoracic and lumbar regions, 60% of the time), as opposed to the upper thoracic (20%) and cervical regions (approximately 15%). Cervical malformations arise from the anterior spinal artery and lie within the cord, whereas thoracolumbar malformations can be internal, external or encompass both areas of the cord.

Malformations can be recognised as part of an acute illness or gradual onset disease. In diseases such as subarachnoid hemorrhage, signs and symptoms include headache, neck stiffness and back and leg pain. Extradural, subdural and intramedullary hematomas are all signs of acute cord compression. Gradual onset diseases are more common (85-90% of all diseases leading to a diagnosis of malformation) and are usually due to an increased venous pressure. Other factors such as thrombosis or arachnoiditis can be involved. A bruit (unusual blood sounds) may be heard overlying the spinal arteriovenous malformation. Very occasionally, nevus (moles) or angiolipomas are found.

Myelography is used to confirm the diagnosis of AVMs and it shows 'snake-like' vessels on the cord's surface. If the myelogram is positive, angiography is required to show the extent of malformation and the exact site of the shunt. Magnetic resonance imaging (MRI) may show the appropriate area. If AVMs are left untreated, 50% of patients with gradual symptoms will be unable to walk within 3 years of onset. Operations can prevent progression and may improve any gait or incontinence.

In 1993, Peter James Dyck divided HSAN I further into five subtypes HSAN IA-E based on the presence of additional features. These features were thought to result from the genetic diversity of HSAN I (i.e. the expression of different genes, different alleles of a single gene, or modifying genes) or environmental factors. Molecular genetic studies later confirmed the genetic diversity of the disease.

Even though clinical diagnostic criteria have not been 100 percent defined for genitopatellar syndrome, the researchers stated that the certain physical features could relate to KAT6B mutation and result in the molecular genetic testing. The researchers stated that the Individuals with two major features or one major feature and two minor features are likely to have a KAT6B mutation.

To diagnose the Genitopatellar Syndrome, there are multiple ways to evaluate.

Medical genetics consultation

- Evaluation by developmental specialist

- Feeding evaluation

- Baseline hearing evaluation

- Thyroid function tests

- Evaluation of males for cryptorchidism

- Orthopedic evaluation if contractures are present or feet/ankles are malpositioned

- Hip radiographs to evaluate for femoral head dislocation

- Renal ultrasound examination for hydronephrosis and cysts

- Echocardiogram for congenital heart defects

- Evaluation for laryngomalacia if respiratory issues are present

- Evaluation by gastroenterologist as needed, particularly if bowel malrotation is suspected

Caudal regression syndrome or sacral agenesis (or hypoplasia of the sacrum) is a congenital disorder in which there is abnormal fetal development of the lower spine—the caudal partition of the spine.

It occurs at a rate of approximately one per 25,000 live births.

Parastremmatic dwarfism is a rare bone disease that features severe dwarfism, thoracic kyphosis (a type of scoliosis that affects the upper back), a distortion and twisting of the limbs, contractures of the large joints, malformations of the vertebrae and pelvis, and incontinence. The disease was first reported in 1970 by Leonard Langer and associates; they used the term "parastremmatic" from the Greek "parastremma", or "distorted limbs", to describe it. On X-rays, the disease is distinguished by a "flocky" or lace-like appearance to the bones. The disease is congenital, which means it is apparent at birth. It is caused by a mutation in the "TRPV4" gene, located on chromosome 12 in humans. The disease is inherited in an autosomal dominant manner.

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.

For most cases the diagnosis for congenital amputation is not made until the infant is born. One procedure that is helpful in determining this condition in an infant is an ultrasound examination of a fetus when still in the mother's abdomen as it can reveal the absence of a limb. However, since ultrasounds are routine they may not pick up all the signs of some of the more subtle birth defects.

The most popular method of treatment for congenital amputation is having the child be fit for a prosthesis which can lead to normal development, so the muscles don't atrophy. If there is congenital amputation of the fingers, plastic surgery can be performed by using the big toe or second toes in place of the missing fingers of the hand.

In rare cases of amniotic banding syndrome, if diagnosed "in utero", fetal surgery may be considered to save a limb which is in danger of amputation.

The diagnosis of IP is established by clinical findings and occasionally by corroborative skin biopsy. Molecular genetic testing of the NEMO IKBKG gene (chromosomal locus Xq28) reveals disease-causing mutations in about 80% of probands. Such testing is available clinically.

In addition, females with IP have skewed X-chromosome inactivation; testing for this can be used to support the diagnosis.

Many people in the past were misdiagnosed with a second type of IP, formerly known as IP1. This has now been given its own name - 'Hypomelanosis of Ito' (incontinentia pigmenti achromians). This has a slightly different presentation: swirls or streaks of hypopigmentation and depigmentation. It is "not" inherited and does not involve skin stages 1 or 2. Some 33–50% of patients have multisystem involvement — eye, skeletal, and neurological abnormalities. Its chromosomal locus is at Xp11, rather than Xq28.

The diagnosis of HSAN I is based on the observation of symptoms described above and is supported by a family history suggesting autosomal dominant inheritance. The diagnosis is also supported by additional tests, such as nerve conduction studies in the lower limbs to confirm a sensory and motor neuropathy. In sporadic cases, acquired neuropathies, such as the diabetic foot syndrome and alcoholic neuropathy, can be excluded by the use of magnetic resonance imaging and by interdisciplinary discussion between neurologists, dermatologists, and orthopedics.

The diagnosis of the disease has been revolutionized by the identification of the causative genes. The diagnosis is now based on the detection of the mutations by direct sequencing of the genes. Nevertheless, the accurate phenotyping of patients remains crucial in the diagnosis. For pregnant patients, termination of pregnancy is not recommended.

HSAN I must be distinguished from hereditary motor and sensory neuropathy (HMSN) and other types of hereditary sensory and autonomic neuropathies (HSAN II-V). The prominent sensory abnormalities and foot ulcerations are the only signs to separate HSAN I from HMSN. HSAN II can be differentiated from HSAN I as it is inherited as an autosomal recessive trait, it has earlier disease onset, the sensory loss is diffused to the whole body, and it has less or no motor symptoms. HSAN III-V can be easily distinguished from HSAN I because of congenital disease onset. Moreover, these types exhibit typical features, such as the predominant autonomic disturbances in HSAN III or congenital loss of pain and anhidrosis in HSAN IV.

Most children with symbrachydactyly have excellent function in daily activities. Due to the length of their arm, they do not qualify for most artificial limbs. However, some adaptive prosthetics and equipment for sports and leisure activities may be helpful when the child is older. Children who demonstrate some functional movement in their remaining fingers and within the palm are evaluated for possible surgery such as toe transfers.

Parastremmatic dwarfism is apparent at birth, with affected infants usually being described as "stiff", or as "twisted dwarfs" when the skeletal deformities and appearance of dwarfism further present themselves. Skeletal deformities usually develop in the sixth to twelfth month of an infant's life. The deformities may be attributed to osteomalacia, a lack of bone mineralization.

The overall prognosis is excellent in most cases. Most children with Adams–Oliver syndrome can likely expect to have a normal life span. However, individuals with more severe scalp and cranial defects may experience complications such as hemorrhage and meningitis, leading to long-term disability.

Spastic quadriplegia can be diagnosed as early as age one after a noticed delay in development, particularly a delay in rolling, crawling, sitting, or walking. However, depending on the severity, signs may not show up until the age of three. Muscle tone is sometimes used to make the diagnosis for spastic quadriplegia as affected children often appear to be either too stiff or too floppy.

Another important diagnostic factor is the persistence of primitive reflexes past the age at which they should have disappeared (6–12 months of age). These reflexes include the rooting reflex, the sucking reflex, and the Moro reflex, among others.

Magnetic resonance imaging (MRI) or a computed tomography scan (CT scan) may be used to locate the cause of the symptoms. Ultrasound may be used for the same function in premature babies.

Because cerebral palsy refers to a group of disorders, it is important to have a clear and systematic naming system. These disorders must be non-progressive, non-transient, and not due to injury to the spinal cord. Disorders within the group are classified based on two characteristics- the main physiological symptom, and the limbs that are affected. For a disorder to be diagnosed as spastic quadriplegia, an individual must show spastic symptoms (as opposed to athetotic, hypertonic, ataxic, or atonic symptoms) and it must be present in all four limbs (as opposed to hemiplegic, diplegic, or triplegic cases).

While a diagnosis may be able to be made shortly after birth based on family history and observation of the infant, it is often postponed until after the child is between 18–24 months old in order to monitor the possible regression or progression of symptoms.