Diagnosis is made through a combination of patient history, neurological examination, and medical imaging. Magnetic resonance imaging (MRI) is considered the best imaging modality for Chiari malformation since it visualizes neural tissue such as the cerebellar tonsils and spinal cord as well as bone and other soft tissues. CT and CT myelography are other options and were used prior to the advent of MRI, but they characterize syringomyelia and other neural abnormalities less well.

By convention the cerebellar tonsil position is measured relative to the basion-opisthion line, using sagittal T1 MRI images or sagittal CT images. The selected cutoff distance for abnormal tonsil position is somewhat arbitrary since not everyone will be symptomatic at a certain amount of tonsil displacement, and the probability of symptoms and syrinx increases with greater displacement, however greater than 5 mm is the most frequently cited cutoff number, though some consider 3–5 mm to be "borderline," and symptoms and syrinx may occur above that. One study showed little difference in cerebellar tonsil position between standard recumbent MRI and upright MRI for patients without a history of whiplash injury. Neuroradiological investigation is used to first rule out any intracranial condition that could be responsible for tonsillar herniation. Neuroradiological diagnostics evaluate the severity of crowding of the neural structures within the posterior cranial fossa and their impact on the foramen magnum. Chiari 1.5 is a term used when both brainstem and tonsillar herniation through the foramen magnum are present.

The diagnosis of a Chiari II malformation can be made prenatally through ultrasound.

In the late 19th century, Austrian pathologist Hans Chiari described seemingly related anomalies of the hindbrain, the so-called Chiari malformations I, II and III. Later, other investigators added a fourth (Chiari IV) malformation. The scale of severity is rated I – IV, with IV being the most severe. Types III and IV are very rare.

Other conditions sometimes associated with Chiari malformation include hydrocephalus, syringomyelia, spinal curvature, tethered spinal cord syndrome, and connective tissue disorders such as Ehlers-Danlos syndrome and Marfan syndrome.

Chiari malformation is the most frequently used term for this set of conditions. The use of the term Arnold–Chiari malformation has fallen somewhat out of favor over time, although it is used to refer to the type II malformation. Current sources use "Chiari malformation" to describe four specific types of the condition, reserving the term "Arnold-Chiari" for type II only. Some sources still use "Arnold-Chiari" for all four types.

Chiari malformation or Arnold–Chiari malformation should not be confused with Budd-Chiari syndrome, a hepatic condition also named for Hans Chiari.

In Pseudo-Chiari Malformation, Leaking of CSF may cause displacement of the cerebellar tonsils and similar symptoms sufficient to be mistaken for a Chiari I malformation.

A doctor will base his or her diagnosis on the symptoms the patient has and the results of tests, including:

- An X-ray

- Magnetic resonance imaging (MRI), which usually provides the most information

- Computed tomography (CT) scan

The earliest point at which a CPAM can be detected is by prenatal ultrasound. The classic description is of an echogenic lung mass that gradually disappears over subsequent ultrasounds. The disappearance is due to the malformation becoming filled with fluid over the course of the gestation, allowing the ultrasound waves to penetrate it more easily and rendering it invisible on sonographic imaging. When a CPAM is rapidly growing, either solid or with a dominant cyst, they have a higher incidence of developing venous outflow obstruction, cardiac failure and ultimately "hydrops fetalis". If "hydrops" is not present, the fetus has a 95% chance of survival. When hydrops is present, risk of fetal demise is much greater without "in utero" surgery to correct the pathophysiology. The greatest period of growth is during the end of the second trimester, between 20–26 weeks.

A measure of mass volume divided by head circumference, termed cystic adenomatoid malformation volume ratio (CVR) has been developed to predict the risk of "hydrops". The lung mass volume is determined using the formula (length × width × anteroposterior diameter ÷ 2), divided by head circumference. With a CVR greater than 1.6 being considered high risk. Fetuses with a CVR less than 1.6 and without a dominant cyst have less than a 3% risk of hydrops. After delivery, if the patient is symptomatic, resection is mandated. If the infant is asymptomatic, the need for resection is a subject of debate, though it is usually recommended. Development of recurrent infections, rhabdomyosarcoma, adenocarcinomas "in situ" within the lung malformation have been reported.

Lymphatic malformations may be detected in the human fetus by ultrasound if they are of sufficient size. Detection of a cystic malformation may prompt further investigation, such as amniocentesis, in order to evaluate for genetic abnormalities in the fetus. Lymphatic malformations may be discovered postnatally or in older children/adults, and most commonly present as a mass or as an incidental finding during medical imaging.

Verification of the diagnosis may require more testing, as there are multiple cystic masses that arise in children. Imaging, such as ultrasound or MRI, may provide more information as to the size and extent of the lesion.

CPAMs are often identified during routine prenatal ultrasonography. Identifying characteristics on the sonogram include: an echogenic (bright) mass appearing in the chest of the fetus, displacement of the heart from its normal position, a flat or everted (pushed downward) diaphragm, or the absence of visible lung tissue.

CPAMs are classified into three different types based largely on their gross appearance. Type I has a large (>2 cm) multiloculated cysts. Type II has smaller uniform cysts. Type III is not grossly cystic, referred to as the "adenomatoid" type. Microscopically, the lesions are not true cysts, but communicate with the surrounding parenchyma. Some lesions have an abnormal connection to a blood vessel from an aorta and are referred to as "hybrid lesions."

Treatment depends on the anatomy of the malformation as determined by angiography or Magnetic Resonance Imaging (MRI).

Cases of lymphangioma are diagnosed by histopathologic inspection. In prenatal cases, cystic lymphangioma is diagnosed using an ultrasound; when confirmed amniocentesis may be recommended to check for associated genetic disorders.

If there aren't neurological symptoms (such as difficulties moving, loss of sensation, confusion, etc.) and there is no evidence of pressure on the spinal cord, a conservative approach may be taken such as:

- Drugs, such as aspirin, without steroids to relieve inflammation

- Cervical traction, in which the neck is pulled along its length, thus relieving pressure on the spinal cord

- Using a neck collar or cervical-thoracic suit

If there is pressure on the spinal cord or life-threatening symptoms are present, surgery is recommended.

The heterogeneity of the Klippel–Feil syndrome has made it difficult to outline the diagnosis as well as the prognosis classes for this disease. Because of this, it has complicated the exact explanation of the genetic cause of the syndrome.

The prognosis for most individuals with KFS is good if the disorder is treated early on and appropriately. Activities that can injure the neck should be avoided, as it may contribute to further damage. Other diseases associated with the syndrome can be fatal if not treated, or if found too late to be treatable.

A doctor can diagnose a stork bite with a simple visual inspection. No tests are needed.

The most accurate method of diagnosis is prenatal screening through real-time fetal images. However, since maternal body habitus leads to diagnostic difficulties using this method, MRI and sonography are the most commonly used technique since there is no exposure to ionizing radiation. At the beginning of the second trimester, the central nervous system (CNS) and anatomic structures of the fetus can be clearly visualized and the characteristic malformations of iniencephaly, such as a shortened trunk, marked lordosis in the cervicothoracic vertebrae, absence or partial absence of the occipital squama, abnoramal fusion of vertebrae, closed vertebral arches, formation of an encephalocele (for iniencephaly apertus), and dorsiflexion of the head in respect to the spine, can be precisely diagnosed as well as the severity and location established. Once established, further decisions can be made with regard to terminating the pregnancy or providing a plan of adequate postnatal care.

The prognosis for lymphangioma circumscriptum and cavernous lymphangioma is generally excellent. This condition is associated with minor bleeding, recurrent cellulitis, and lymph fluid leakage. Two cases of lymphangiosarcoma arising from lymphangioma circumscriptum have been reported; however, in both of the patients, the preexisting lesion was exposed to extensive radiation therapy.

In cystic hygroma, large cysts can cause dysphagia, respiratory problems, and serious infection if they involve the neck. Patients with cystic hygroma should receive cytogenetic analysis to determine if they have chromosomal abnormalities, and parents should receive genetic counseling because this condition can recur in subsequent pregnancies.

Complications after surgical removal of cystic hygroma include damage to the structures in the neck, infection, and return of the cystic hygroma.

Physicians now use magnetic resonance imaging (MRI) to diagnose syringomyelia. The MRI radiographer takes images of body anatomy, such as the brain and spinal cord, in vivid detail. This test will show the syrinx in the spine or any other conditions, such as the presence of a tumor. MRI is safe, painless, and informative and has greatly improved the diagnosis of syringomyelia.

The physician may order additional tests to help confirm the diagnosis. One of these is called electromyography (EMG), which show possible lower motor neuron damage. In addition, computed axial tomography (CT) scans of a patient's head may reveal the presence of tumors and other abnormalities such as hydrocephalus.

Like MRI and CT scans, another test, called a myelogram, uses radiographs and requires a contrast medium to be injected into the subarachnoid space. Since the introduction of MRI this test is rarely necessary to diagnose syringomyelia.

The possible causes are trauma, tumors and congenital defects. It is most usually observed in the part of the spinal cord corresponding to the neck area. Symptoms are due to spinal cord damage and are: pain, decreased sensation of touch, weakness and loss of muscle tissue. The diagnosis is confirmed with a spinal CT, myelogram or MRI of the spinal cord. The cavity may be reduced by surgical decompression.

Furthermore, evidence also suggests that impact injuries to the thorax area highly correlate with the occurrence of a cervical-located syrinx.

Treatment for Klippel–Feil syndrome is symptomatic and may include surgery to relieve cervical or craniocervical instability and constriction of the spinal cord, and to correct scoliosis.

Failing non-surgical therapies, spinal surgery may provide relief. Adjacent segment disease and scoliosis are two examples of common symptoms associated with Klippel–Feil syndrome, and they may be treated surgically. The three categories treated for types of spinal cord deficiencies are massive fusion of the cervical spine (Type I), the fusion of 1 or 2 vertebrae (Type II), and the presence of thoracic and lumbar spine anomalies in association with type I or type II Klippel–Feil syndrome (Type III).

Adjacent segment disease can be addressed by performing cervical disc arthroplasty using a device such as the Bryan cervical disc prosthesis.

The option of the surgery is to maintain range of motion and attenuate the rate of adjacent segment disease advancement without fusion.

Another type of arthroplasty that is becoming an alternate choice to spinal fusion is Total Disc Replacement. Total disc replacement objective is to reduce pain or eradicate it.

Spinal fusion is commonly used to correct spinal deformities such as scoliosis. Arthrodesis is the last resort in pain relieving procedures, usually when arthroplasties fail.

Since many of the characteristics of iniencephaly, such as congenital retroflexion of the spine and fusion of the cervical vertebrae, are shared with other disorders, key differences are important to note.

While anencephaly experiences a partial to total lack of the neurocranium, iniencephaly does not. In anencephaly, the retroflexed head is not covered with skin while in iniencephaly, the retroflexed head is covered with skin entirely. Cervical vertebrae are malformed and reduced in iniencephaly while they are almost normal in anencephaly.

Even though KFS does experience malformed cervical vertebra due to failure of segmentation during early fetal development, there is not retroflexion of the head as seen in iniencephaly. While iniencephaly clausus is fatal, KFS is not and can be surgically corrected. Therefore, it is crucial to correctly diagnose KFS and not mistake it for iniencephaly clausus.

A baby with a prenatally diagnosed cystic hygroma should be delivered in a major medical center equipped to deal with neonatal complications, such as a neonatal intensive care unit. An obstetrician usually decides the method of delivery. If the cystic hygroma is large, a cesarean section may be performed. After birth, infants with a persistent cystic hygroma must be monitored for airway obstruction. A thin needle may be used to reduce the volume of the cystic hygroma to prevent facial deformities and airway obstruction. Close observation of the baby by a neonatologist after birth is recommended. If resolution of the cystic hygroma does not occur before birth, a pediatric surgeon should be consulted.

Cystic hygromas that develop in the third trimester, after thirty weeks gestation, or in the postnatal period are usually not associated with chromosome abnormalities. There is a chance of recurrence after surgical removal of the cystic hygroma. The chance of recurrence depends on the extent of the cystic hygroma and whether its wall was able to be completely removed.

Treatments for removal of cystic hygroma are surgery or sclerosing agents which include:

- Bleomycin

- Doxycycline

- Ethanol (pure)

- Picibanil (OK-432)

- Sodium tetradecyl sulfate

There is no cure for this condition. Treatment is supportive and varies depending on how symptoms present and their severity. Some degree of developmental delay is expected in almost all cases of M-CM, so evaluation for early intervention or special education programs is appropriate. Rare cases have been reported with no discernible delay in academic or school abilities.

Physical therapy and orthopedic bracing can help young children with gross motor development. Occupational therapy or speech therapy may also assist with developmental delays. Attention from an orthopedic surgeon may be required for leg length discrepancy due to hemihyperplasia.

Children with hemihyperplasia are thought to have an elevated risk for certain types of cancers. Recently published management guidelines recommend regular abdominal ultrasounds up to age eight to detect Wilms' tumor. AFP testing to detect liver cancer is not recommended as there have been no reported cases of hepatoblastoma in M-CM patients.

Congenital abnormalities in the brain and progressive brain overgrowth can result in a variety of neurological problems that may require intervention. These include hydrocephalus, cerebellar tonsillar herniation (Chiari I), seizures and syringomyelia. These complications are not usually congenital, they develop over time often presenting complications in late infancy or early childhood, though they can become problems even later. Baseline brain and spinal cord MRI imaging with repeat scans at regular intervals is often prescribed to monitor the changes that result from progressive brain overgrowth.

Assessment of cardiac health with echocardiogram and EKG may be prescribed and arrhythmias or abnormalities may require surgical treatment.

Testing for a malformed vein of Galen is indicated when a patient has heart failure which has no obvious cause. Diagnosis is generally achieved by signs such as cranial bruits and symptoms such as expanded facial veins. The vein of Galen can be visualized using ultrasound or Doppler. A malformed Great Cerebral Vein will be noticeably enlarged. Ultrasound is a particularly useful tool for vein of Galen malformations because so many cases occur in infancy and ultrasound can make diagnoses prenatally. Many cases are diagnosed only during autopsy as congestive heart failure occurs very early.

An AVM diagnosis is established by neuroimaging studies after a complete neurological and physical examination. Three main techniques are used to visualize the brain and search for AVM: computed tomography (CT), magnetic resonance imaging (MRI), and cerebral angiography. A CT scan of the head is usually performed first when the subject is symptomatic. It can suggest the approximate site of the bleed. MRI is more sensitive than CT in the diagnosis of AVMs and provides better information about the exact location of the malformation. More detailed pictures of the tangle of blood vessels that compose an AVM can be obtained by using radioactive agents injected into the blood stream. If a CT is used in conjunctiangiogram, this is called a computerized tomography angiogram; while, if MRI is used it is called magnetic resonance angiogram. The best images of an AVM are obtained through cerebral angiography. This procedure involves using a catheter, threaded through an artery up to the head, to deliver a contrast agent into the AVM. As the contrast agent flows through the AVM structure, a sequence of X-ray images are obtained.

Most countries have standard newborn exams that include a hip joint exam screening for early detection of hip dysplasia.

Sometimes during an exam a "click" or more precisely "clunk" in the hip may be detected (although not all clicks indicate hip dysplasia). When a hip click (also known as "clicky hips" in the UK) is detected, the child's hips are tracked with additional screenings to determine if developmental dysplasia of the hip is caused.

Two maneuvers commonly employed for diagnosis in neonatal exams are the Ortolani maneuver and the Barlow maneuver.

In order to do the Ortolani maneuver it is recommended that the examiner put the newborn baby in a position in which the contralateral hip is held still while the thigh of the hip being tested is abducted and gently pulled anteriorly. If a "clunk" is heard (the sound of the femoral head moving over the acetabulum), the joint is normal, but absence of the "clunk" sound indicates that the acetabulum is not fully developed. The next method that can be used is called the Barlow maneuver. It is done by adducting the hip while pushing the thigh posteriorly. If the hip goes out of the socket it means it is dislocated, and the newborn has a congenital hip dislocation. The baby is laid on its back for examination by separation of its legs. If a clicking sound can be heard, it indicates that the baby may have a dislocated hip. It is highly recommended that these maneuvers be done when the baby is not fussing, because the baby may inhibit hip movement.

The condition can be confirmed by ultrasound and X-ray. Ultrasound imaging yields better results defining the anatomy until the cartilage is ossified. When the infant is around 3 months old a clear roentgenographic image can be achieved. Unfortunately the time the joint gives a good x-ray image is also the point at which nonsurgical treatment methods cease to give good results. In x-ray imaging dislocation may be indicated if the Shenton's line (an arc drawn from the medial aspect of the femoral neck through the superior margin of the obturator foramen) does not result in a smooth arc. However, in infants this line can be unreliable as it depends on the rotation of the hip when the image is taken ()

Asymmetrical gluteal folds and an apparent limb-length inequality can further indicate unilateral hip dysplasia. Most vexingly, many newborn hips show a certain ligamentous laxity, on the other hand severely malformed joints can appear stable. That is one reason why follow-up exams and developmental monitoring are important. Frequency and methods of routine screenings in children is still in debate however physical examination of newborns followed by appropriate use of hip ultrasound is widely accepted.

The Harris hip score (developed by William H. Harris MD, an orthopedist from Massachusetts) is one way to evaluate hip function following surgery. Other scoring methods are based on patients' evaluation like e.g. the Oxford hip score, HOOS and WOMAC score. Children's Hospital Oakland Hip Evaluation Scale (CHOHES) is a modification of the Harris hip score that is currently being evaluated.

Hip dysplasia can develop in older age. Adolescents and adults with hip dysplasia may present with hip pain and in some cases hip labral tears. X-rays are used to confirm a diagnosis of hip dysplasia. CT scans and MRI scans are occasionally used too.

Most stork bites on the face go away completely in about 18 months. Stork bites on the back of the neck usually do not go away.

The diagnosis of Carpenter Syndrome is made based on the presence of the bicoronal and sagittal skull malformations, which results in a pointed, cone-shaped or short, broad head. The diagnosis is also made based on the presence of extra or fused digits. X rays and/ or CT scans of the skull may be performed in order to accurately diagnose the individual; however, other genetic disorders, which have available genetic tests, are also characterized by skull malformations. A positive result on these tests can rule out a Carpenter Syndrome diagnosis.

The indication to surgically stabilize a cervical fracture can be estimated from the "Subaxial Injury Classification" (SLIC). In this system, a score of 3 or less indicates that conservative management is appropriate, a score of 5 or more indicates that surgery is needed, and a score of 4 is equivocal. The score is the sum from 3 different categories: morphology, discs and ligaments, and neurology:

In 1979 Dr. John F. Crowe et al. proposed a classification to define the degree of malformation and dislocation. Grouped from least severe Crowe I dysplasia to most severe Crowe IV. This classification is very useful for studying treatment results.

Rather than using the Wiberg angle because it makes it difficult to quantify the degree of dislocation they used 3 key elements to determine the degree of subluxation: A reference line at the lower rim of the "teardrop", junction between the femoral head and neck of the respective joint and the height of the pelvis (vertical measurement). They studied anteroposterior pelvic x-rays and drew horizontal lines through the lower rim of a feature called "teardrop". The distance between this line and the middle lines of the junction between femur head and neck gave them a measure of the degree of femur head subluxation. They further established that a "normal" diameter of the femur head measures 20% of the height of the pelvis. If the middle line of the neck-head junction was more than 10% of the pelvis height above the reference line they considered the joint to be more than 50% dislocated.

The following types resulted: