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.

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.

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.

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.

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

Macrocephaly is customarily diagnosed if head circumference is greater than two standard deviations (SDs) above the mean. Relative macrocephaly occurs if the measure is less than two SDs above the mean, but is disproportionately above that when ethnicity and stature are considered. In research, cranial height or brain imaging is also used to determine intracranial volume more accurately.

The differential diagnoses are extensive and include: Alagille syndrome, alpha-1-antitrypsin deficiency, Byler disease (progressive familial intrahepatic cholestasis), Caroli disease, choledochal cyst, cholestasis, congenital cytomegalovirus disease, congenital herpes simplex virus infection, congenital rubella, congenital syphilis, congenital toxoplasmosis, cystic fibrosis, galactosemia, idiopathic neonatal hepatitis, lipid storage disorders, neonatal hemochromatosis, and total parenteral nutrition-associated cholestasis.

Craniometaphyseal dysplasia is diagnosed based on clinical and radiographic findings that include hyperostosis. Some things such as cranial base sclerosis and nasal sinuses obstruction can be seen during the beginning of the child's life. In radiographic findings the most common thing that will be found is the narrowing of foramen magnum and the widening of long bones. Once spotted treatment is soon suggested to prevent further compression of the foramen magnum and disabling conditions.

Prognosis varies widely depending on severity of symptoms, degree of intellectual impairment, and associated complications. Because the syndrome is rare and so newly identified, there are no long term studies.

Once the diagnosis of polymicrogyria has been established in an individual, the following approach can be used for discussion of prognosis:

A pregnancy history should be sought, with particular regard to infections, trauma, multiple gestations, and other documented problems. Screening for the common congenital infections associated with polymicrogyria with standard TORCH testing may be appropriate. Other specific tests targeting individual neurometabolic disorders can be obtained if clinically suggested.

The following may help in determining a genetic etiology:

Family history

It is important to ask for the presence of neurologic problems in family members, including seizures, cognitive delay, motor impairment, pseudobulbar signs, and focal weakness because many affected family members, particularly those who are older, may not have had MRI performed, even if these problems came to medical attention. In addition, although most individuals with polymicrogyria do present with neurologic difficulties in infancy, childhood, or adulthood, those with mild forms may have no obvious deficit or only minor manifestations, such as a simple lisp or isolated learning disability. Therefore, if a familial polymicrogyria syndrome is suspected, it may be reasonable to perform MRI on relatives who are asymptomatic or have what appear to be minor findings. The presence of consanguinity in a child's parents may suggest an autosomal recessive familial polymicrogyria syndrome.

Physical examination

A general physical examination of the proband may identify associated craniofacial, musculoskeletal, or visceral malformations that could indicate a particular syndrome. Neurologic examination should assess cognitive and mental abilities, cranial nerve function, motor function, deep tendon reflexes, sensory function, coordination, and gait (if appropriate).

Genetic testing

Diagnosis is made by an assessment of symptoms, physical exam, and medical history, in conjunction with blood tests, a liver biopsy, and imaging. Diagnosis is often made following investigation of prolonged jaundice that is resistant to phototherapy and/or exchange transfusions, with abnormalities in liver enzyme tests. Ultrasound or other forms of imaging can confirm the diagnosis. Further testing may include radioactive scans of the liver and a liver biopsy.

Kaposiform hemangioendothelioma (KHE) is a rare vascular neoplasm that is locally aggressive but without metastatic potential. It occurs particularly in the skin, deep soft tissue, retroperitoneum, mediastinum, and rarely in bone. Although lesions occur solitary, they often involve large areas of the body, such as the head/neck region (40%), trunk (30%), or extremity (30%).

Usually, it is present at birth as a flat, reddish-purple, tense and edematous lesion.

Although half of lesions are congenital, 58% of KHE develop during infancy, 32% between age 1 and 10 years (32%) and 10% after 11 years of age. Moreover, adult onset has been described too with mainly males being affected. Both sexes are affected equally in children.

Lesions are often greater than 5 cm in diameter and can cause visible deformity and pain. During early childhood, KHE may enlarge and after 2 years of age, it may partially regress. Though, it usually persists longterm. In addition, 50% of patients suffer from coagulopathy due to thrombocytopenia (<25,000/mm3), presenting with petechiae and bleeding. This is called the Kasabach-Merritt Phenomenon, which is caused by trapping of platelets and other clotting factors within the tumor. Kasabach-Merritt Phenomenon is less likely in patients with lesions less than 8 cm. As two-thirds of adult-onset KHE tumors are less than 2 cm, KHE in adults is rarely associated with Kasabach-Merritt Phenomenon.

Patients with KHE and Kasabach-Merritt Phenomenon present with petechiae and ecchymosis.

Most KHE tumors are diffuse involving multiple tissue planes and important structures. Resection of KHE is thus often difficult. Treatment of kaposiform hemangioendothelioma is therefore medical. The primary drug is interferon alfa, which is successful in 50% of children. Another option is vincristine, which has lots of side-effects, but has a response rate of 90%. Drug therapy is often used in shrinking the tumor and treating the coagulopathy. However, many of these kaposiform hemangioendotheliomas do not completely regress and remain as a much smaller asymptomatic tumor. However, KHE still has a high mortality rate of 30%. Although complete surgical removal with a large margin has the best reported outcome, it is usually not done because of the risk of bleeding, extensiveness, and the anatomic site of the lesion.

Operative management may be possible for small or localized lesions. Removal of larger areas also may be indicated for symptomatic patients or for patients who have failed farmacotherapy. Resection is not required for lesions that are not causing functional problems, because KHE is benign and because resection could cause deformity.

The only treatment for this disorder is surgery to reduce the compression of cranial nerves and spinal cord. However, bone regrowth is common since the surgical procedure can be technically difficult. Genetic counseling is offered to the families of the people with this disorder.

Congenital hemangioma can be distinguished from infantile hemangioma because it is fully developed at birth. It forms during prenatal life and has reached its maximal size at birth. Congenital hemangioma can even be diagnosed in utero by prenatal ultrasound. Unlike IH, CH is more common in the extremities, has an equal sex distribution, and is solitary, with an average diameter of 5 cm. It commonly presents in the head and neck and in the lower extremities.

Congenital hemangioma are divided into 2 subgroups: the rapidly involuting congenital hemangiomas (RICHs) and the non-involuting congenital hemangiomas(NICHs).

The rapidly involuting congenital hemangioma, RICH, presents at birth as a solitary raised tumor with a central depression, scar, or ulceration surrounded by a rim of pallor. It is noted for its involution, which typically begins several weeks after birth and is completed no later than 14 months of age. After regression RICH may cause a residual deformity, such as atrophic skin and subcutaneous tissue. It mainly affects the limbs (52%), but also the head and neck region (42%) and the trunk (6%).

The non-involuting congenital hemangioma, NICH, presents as a solitary, well-circumscribed reddish-pink to purple plaque with central telangiectasia and hypopigmented rim. In contrast to RICH, NICH does not involute and rarely ulcerates. It persists into late childhood and can even mimic a vascular malformation by growing commensurately with the child. Although NICH can resemble RICH in its external appearance, it can be differentiated from RICH by a greater elevation and coarse telangiectases. It mainly affects the head and neck region (43%), but also the limbs (38%) and the trunk (19%).

Surgical resection for congenital hemangiomas is rarely needed, because RICH undergoes postnatal regression and NICH is benign and often asymptomatic. Resection may be indicated to improve the appearance of the affected area, as long as the surgical scar is less noticeable than the lesion. Other indications are problematic ulcers with persistent bleeding or chronic infection.

Although most NICH lesions are non-problematic and do not cause significant deformity, the threshold for resection of NICH is lower, because it neither involutes, nor responds to pharmacotherapy. RICH tumors are observed until involution is completed. Involuted RICH may leave behind atrophic tissue, which can be reconstructed with autologous grafts. It is often best to postpone excision until regression is complete.

There are effective pharmacologic treatments, which include intralesional corticosteroid injection, systemic corticosteroid injection, interferon α-2a or α-2b and angiogenic inhibitors. The use of corticosteroids leads to accelerated regression in 30%, stabilization of growth in 40%, lightening of color and softening of the tumor. However, 30% shows minimal or no response. Another drug treatment is interferon α-2a or α-2b. It is often used for patients who did not respond to corticosteroids. Although the response rate is much slower, it has been successful for 80% of children treated. The most serious side effect of interferon is a spastic diplegia. Other therapeutic options are embolization and pulsed-dye laser, which improves residual telangiectasias in RICH and in NICH.

Surgical correction is recommended when a constriction ring results in a limb contour deformity, with or without lymphedema.

Genetic counseling for VWS involves discussion of disease transmission in the autosomal dominant manner and possibilities for penetrance and expression in offspring. Autosomal dominance means affected parents have a 50% chance of passing on their mutated "IRF6" allele to a their child. Furthermore, if a cleft patient has lip pits, he or she has a ten times greater risk of having a child with cleft lip with or without cleft palate than a cleft patient who does not have lip pits. Types of clefting between parents and affected children are significantly associated; however, different types of clefts may occur horizontally and vertically within the same pedigree. In cases where clefting is the only symptom, a complete family history must be taken to ensure the patient does not have non-syndromic clefting.

Weissenbacher-Zweymüller syndrome is diagnosed upon a thorough clinical evaluation, detailed patient history, identification of characteristic symptom and a variety of specialized tests which includes x-rays.

Fetal and neonatal intestinal atresia are treated using laparotomy after birth. If the area affected is small, the surgeon may be able to remove the damaged portion and join the intestine back together. In instances where the narrowing is longer, or the area is damaged and cannot be used for period of time, a temporary stoma may be placed.

Parents of a proband

- The parents of an affected individual are obligate heterozygotes and therefore carry one mutant allele.

- Heterozygotes (carriers) are asymptomatic.

Sibs of a proband

- At conception, each sibling of an affected individual has a 25% chance of being affected, a 50% chance of being an asymptomatic carrier, and a 25% chance of being unaffected and not a carrier.

- Once an at-risk sibling is known to be unaffected, the risk of his/her being a carrier is 2/3.

- Heterozygotes (carriers) are asymptomatic.

Offspring of a proband

- Offspring of a proband are obligate heterozygotes and will therefore carry one mutant allele.

- In populations with a high rate of consanguinity, the offspring of a person with GPR56-related BFPP and a reproductive partner who is a carrier of GPR56-related BFPP have a 50% chance of inheriting two GPR56 disease-causing alleles and having BFPP and a 50% chance of being carriers.

Other family members of a proband.

- Each sibling of the proband's parents is at a 50% risk of being a carrier

At the beginning of the surgery a tourniquet will be applied to the limb. A tourniquet compresses and control the arterial and venous circulation for about 2 hours. The constriction band must be dissected very carefully to avoid damaging the underlying neurovasculature. When the constriction band is excised, there will be a direct closure. This allows the fatty tissue to naturally reposition itself under the skin.

“With complete circumferential constriction bands, it is recommended that a two-stage correction approach be used. At the first operation, one-half of the circumference is excised and the other one-half can be excised after three to six months. This will avoid any problems to the distal circulation in the limb, which may already be compromised. Lymphedema, when present, will significantly improve within a few weeks of the first surgery.”

For the direct closure of the defect after dissecting a constriction band there are two different techniques:

1. Triangular flaps; For this technique the circumference between the two borders must be measured. Depending on the difference the number of triangular flaps can be decided. With a triangular flap you can create more skin.

2. Z/W-plasty; “Z-plasty is a plastic surgery technique that is used to improve the functional and cosmetic appearance of scars. It can elongate a contracted scar or rotate the scar tension line. The middle line of the Z-shaped incision (the central element) is made along the line of greatest tension or contraction, and triangular flaps are raised on opposite sides of the two ends and then transposed.”

In rare cases, if diagnosed in utero, fetal surgery may be considered to save a limb that is in danger of amputation or other deformity. This operation has been successfully performed on fetuses as young as 22 weeks. The Melbourne's Monash Medical Centre in Australia, as well as multiple facilities in the United States of America, have performed successful amniotic band release surgery.

Modeling EEC syndrome in vitro has been achieved by reprogramming EEC fibroblasts carrying mutations R304W and R204W into induced pluripotent stem cell (iPSC) lines. EEC-iPSC recapitulated defective epidermal and corneal fates. This model further identified PRIMA-1MET, a small compound that was identified as a compound targeting and reactivating p53 mutants based on a cell-based screening for rescuing the apoptotic activity of p53, as efficient to rescue R304W mutation defect. Of interest, similar effect had been observed on keratinocytes derived from the same patients. PRIMA-1MET could become an effective therapeutic tool for EEC patients.

Further genetic research is necessary to identify and rule out other possible loci contributing to EEC syndrome, though it seems certain that disruption of the p63 gene is involved to some extent. In addition, genetic research with an emphasis on genetic syndrome differentiation should prove to be very useful in distinguishing between syndromes that present with very similar clinical findings. There is much debate in current literature regarding clinical markers for syndromic diagnoses. Genetic findings could have great implications in clinical diagnosis and treatment of not only EEC, but also many other related syndromes.

Lip pits may be surgically removed either for aesthetic reasons or discomfort due to inflammation caused by bacterial infections or chronic saliva excretion, though spontaneous shrinkage of the lip pits has occurred in some rare cases. Chronic inflammation has also been reported to cause squamous-cell carcinoma. It is essential to completely remove the entire lip pit canal, as mucoid cysts can develop if mucous glands are not removed. A possible side effect of removing the lip pits is a loose lip muscle. Other conditions associated with VWS, including CL, CP, congenital heart defects, etc. are surgically corrected or otherwise treated as they would be if they were non-syndromic.

Radiographic analysis by performing a computed axial tomographic scan is the gold standard for diagnosing craniosynostosis.

Plain radiography of the skull may be sufficient for diagnosing a single suture craniosynostosis and should therefore be performed, but the diagnostic value is outweighed by that of the CT-scan. Not only can the sutures be identified more accurately, thus objectively demonstrating a fused suture, but also evaluation of the brain for structural abnormalities and excluding other causes of asymmetric growth are possible at the same time. In addition to this, CT-scanning can visualize the extent of skull deformity, thereby enabling the surgeon to start planning surgical reconstruction.

Diagnosis can be characterized by typical facial and cranial deformities.

Observatory signs of trigonocephaly are:

- a triangular shaped forehead seen from top view leading to a smaller anterior cranial fossa

- a visible and palpable midline ridge

- hypotelorism inducing ethmoidal hypoplasia

Imaging techniques (3D-CT, Röntgenography, MRI) show:

- epicanthal folds in limited cases

- teardrop shaped orbits angulated towards the midline of the forehead ('surprised coon' sign) in severe cases

- a contrast difference between a röntgenograph of a normal and a trigonocephalic skull

- anterior curving of the metopic suture seen from lateral view of the cranium on a röntgenograph

- a normal cephalic index (maximum cranium width / maximum cranium length) however, there is bitemporal shortening and biparietal broadening

The neuropsychological development is not always affected. These effects are only visible in a small percentage of children with trigonocephaly or other suture synostoses. Neuropsychological signs are:

- problems in behaviour, speech and language

- mental retardation

- neurodevelopmental delays such as ADHD (Attention Deficit Hyperactivity Disorder), ODD (Oppositional Defiant Disorder), ASD (Autism Spectrum Disorder) and CD (Conduct Disorder). Many of these delays become evident at school age.

Aphalangy, hemivertebrae and urogenital-intestinal dysgenesis is an extremely rare syndrome, described only in three siblings. It associates hypoplasia or aplasia of phalanges of hands and feet, hemivertebrae and various urogenital and/or intestinal abnormalities. Intrafamilial variability is important as one sister had lethal abnormalities (Potter sequence and pulmonary hypoplasia), while her affected brother was in good health with normal psychomotor development at 6 months of age. Prognosis seems to depend mainly on the severity of visceral malformations. Etiology and inheritance remain unknown.