Diagnosis may be delayed for several months because the infant's early behavior appears to be relatively normal. Transillumination, an examination in which light is passed through body tissues, can be used to diagnose hydranencephaly. An accurate, confirmed diagnosis is generally impossible until after birth, though prenatal diagnosis using fetal ultrasonography (ultrasound) can identify characteristic physical abnormalities that exist. Through thorough clinical evaluation, via physical findings, detailed patient history, and advanced imaging techniques, such as angiogram, computerized tomography (CT scan), magnetic resonance imaging (MRI), or more rarely transillumination after birth are the most accurate diagnostic techniques. However, diagnostic literature fails to provide a clear distinction between severe obstructive hydrocephalus and hydranencephaly, leaving some children with an unsettled diagnosis.

Preliminary diagnosis may be made in utero via standard ultrasound, and can be confirmed with a standard anatomy ultrasound. This sometimes proves to provide a misdiagnosis of differential diagnoses including bilaterally symmetric schizencephaly (a less destructive developmental process on the brain), severe hydrocephalus (cerebrospinal fluid excess within the skull), and alobar holoprosencephaly (a neurological developmental anomaly). Once destruction of the brain is complete, the cerebellum, midbrain, thalami, basal ganglia, choroid plexus, and portions of the occipital lobes typically remain preserved to varying degrees. Though the cerebral cortex is absent, in most cases the fetal head remains enlarged due to the continued production by the choroid plexus of cerebrospinal fluid that is inadequately reabsorbed causing increased intracranial pressure.

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.

Open spina bifida can usually be detected during pregnancy by fetal ultrasound. Increased levels of maternal serum alpha-fetoprotein (MSAFP) should be followed up by two tests – an ultrasound of the fetal spine and amniocentesis of the mother's amniotic fluid (to test for alpha-fetoprotein and acetylcholinesterase). AFP tests are now mandated by some state laws (including California). and failure to provide them can have legal ramifications. In one case, a man born with spina bifida was awarded a $2-million settlement after court found his mother's OBGYN negligent for not performing these tests. Spina bifida may be associated with other malformations as in dysmorphic syndromes, often resulting in spontaneous miscarriage. In the majority of cases, though, spina bifida is an isolated malformation.

Genetic counseling and further genetic testing, such as amniocentesis, may be offered during the pregnancy, as some neural tube defects are associated with genetic disorders such as trisomy 18. Ultrasound screening for spina bifida is partly responsible for the decline in new cases, because many pregnancies are terminated out of fear that a newborn might have a poor future quality of life. With modern medical care, the quality of life of patients has greatly improved.

Diagnosing colpocephaly prenatally is difficult because in many cases signs start to appear after birth. Prenatal diagnosis is made by detecting enlargement of either or both occipital horns of the lateral ventricles. Usually prenatal ultrasounds don't show cephalic abnormalities and in cases that they do show abnormality is of low accuracy, making it difficult to diagnose colpocephaly. Often, abnormalities in prenatal ultrasounds can be misdiagnosed as hydrocephalus.

After birth, MR imaging can be done to look for cephalic abnormalities. This is the most commonly used method for diagnosing colpocephaly. Physicians look for abnormally large occipital horns of the lateral ventricles and diminished thickness of white matter. Spinal tapping is not a preferred method for diagnosis because newborn babies with colpocephaly or hydrocephaly have open fontanelles which makes it difficult to collect CSF. Also, colpocephaly is not associated with increased pressure.

Phase contrast-MRI is an imaging method which is more sensitive than MRI for analysis of the pulsatile CSF flow in the ventricular system. This method takes multiple images of the ventricles within one cardiac cycle to measure the flow of CSF running past the area of acquisition. If no flow is seen, this is a reliable diagnosis of aqueductal stenosis as it implies that there is a blockage of CSF.

Ultrasonography can be used in utero to diagnose aqueductal stenosis by showing dilation of the lateral and third ventricles. A retrospective study found that diagnosis can be made as early as 19 weeks of gestation, and that on average diagnosis is made at 33 weeks. Unfortunately, prenatal diagnosis still has a poor prognosis even with immediate treatment upon birth.

MRI is considered the best method of detecting aqueductal stensosis because it can visualize the entire length of the aqueduct, can clearly depict tumors, and can show ventricle enlargement or other deformations. It is helpful in determining the extent of the aqueductal obstruction, particularly when multiple masses or lesions are present, and thereby aids in determining the most appropriate treatment method (i.e. surgery, shunt, or ETV). When constructive interference in steady state (CISS) or fast imaging employing steady-state acquisition (FIESTA) sequence are used, subtle abnormalities or partial obstructions in the aqueduct can be depicted in the MRI. For example, CISS can be used to determine if a thin membrane interfering with CSF flow is present.

There is no standard treatment for hydranencephaly. Treatment is symptomatic and supportive. Hydrocephalus may be treated with surgical treatment of a shunt, which often grants a much better prognosis and greater quality of life.

The prognosis for children with hydranencephaly is generally quite poor. Death often occurs in the first year of life, but other children may live several years.

Medical text identifies that hydranencephalic children simply have only their brain stem function remaining, thus leaving formal treatment options as symptomatic and supportive. Severe hydrocephalus causing macrocephaly, a larger than average head circumference, can easily be managed by placement of a shunt and often displays a misdiagnosis of another lesser variation of cephalic condition due to the blanketing nature of hydrocephalus. Plagiocephaly, the asymmetrical distortion of the skull, is another typical associated condition that is easily managed through positioning and strengthening exercises to prevent torticollis, a constant spasm or extreme tightening of the neck muscles.

Examples of possible complications include shunt malfunction, shunt failure, and shunt infection, along with infection of the shunt tract following surgery (the most common reason for shunt failure is infection of the shunt tract). Although a shunt generally works well, it may stop working if it disconnects, becomes blocked (clogged), infected, or it is outgrown. If this happens the cerebrospinal fluid will begin to accumulate again and a number of physical symptoms will develop (headaches, nausea, vomiting, photophobia/light sensitivity), some extremely serious, like seizures. The shunt failure rate is also relatively high (of the 40,000 surgeries performed annually to treat hydrocephalus, only 30% are a patient's first surgery) and it is not uncommon for patients to have multiple shunt revisions within their lifetime.

Another complication can occur when CSF drains more rapidly than it is produced by the choroid plexus, causing symptoms - listlessness, severe headaches, irritability, light sensitivity, auditory hyperesthesia (sound sensitivity), nausea, vomiting, dizziness, vertigo, migraines, seizures, a change in personality, weakness in the arms or legs, strabismus, and double vision - to appear when the patient is vertical. If the patient lies down, the symptoms usually vanish quickly. A CT scan may or may not show any change in ventricle size, particularly if the patient has a history of slit-like ventricles. Difficulty in diagnosing overdrainage can make treatment of this complication particularly frustrating for patients and their families. Resistance to traditional analgesic pharmacological therapy may also be a sign of shunt overdrainage "or" failure.

The diagnosis of cerebrospinal fluid buildup is complex and requires specialist expertise. Diagnosis of the particular complication usually depends on when the symptoms appear - that is, whether symptoms occur when the patient is upright or in a prone position, with the head at roughly the same level as the feet.

There is neither a single cause of spina bifida nor any known way to prevent it entirely. However, dietary supplementation with folic acid has been shown to be helpful in reducing the incidence of spina bifida. Sources of folic acid include whole grains, fortified breakfast cereals, dried beans, leaf vegetables and fruits.

Folate fortification of enriched grain products has been mandatory in the United States since 1998. The U.S. Food and Drug Administration, Public Health Agency of Canada and UK recommended amount of folic acid for women of childbearing age and women planning to become pregnant is at least 0.4 mg/day of folic acid from at least three months before conception, and continued for the first 12 weeks of pregnancy.

Women who have already had a baby with spina bifida or other type of neural tube defect, or are taking anticonvulsant medication, should take a higher dose of 4–5 mg/day.

Certain mutations in the gene "VANGL1" have been linked with spina bifida in some families with a history of the condition.

Hydrocephalus can be successfully treated by placing a drainage tube (shunt) between the brain ventricles and abdominal cavity. There is some risk of infection being introduced into the brain through these shunts, however, and the shunts must be replaced as the person grows. A subarachnoid hemorrhage may block the return of CSF to the circulation.

This should be distinguished from external hydrocephalus. This is a condition generally seen in infants and involving enlarged fluid spaces or subarachnoid spaces around the outside of the brain. This is generally a benign condition that resolves spontaneously by 2 years of age. (Greenberg, Handbook of Neurosurgery, 5th Edition, pg 174). Imaging studies and a good medical history can help to differentiate external hydrocephalus from subdural hemorrhages or symptomatic chronic extra-axial fluid collections which are accompanied by vomiting, headaches and seizures.

Hydrocephalus treatment is surgical, creating a way for the excess fluid to drain away. In the short term, an external ventricular drain (EVD), also known as an extraventricular drain or ventriculostomy, provides relief. In the long term, some patients will need any of various types of cerebral shunt. It involves the placement of a ventricular catheter (a tube made of silastic) into the cerebral ventricles to bypass the flow obstruction/malfunctioning arachnoidal granulations and drain the excess fluid into other body cavities, from where it can be resorbed. Most shunts drain the fluid into the peritoneal cavity (ventriculo-peritoneal shunt), but alternative sites include the right atrium (ventriculo-atrial shunt), pleural cavity (ventriculo-pleural shunt), and gallbladder. A shunt system can also be placed in the lumbar space of the spine and have the CSF redirected to the peritoneal cavity (Lumbar-peritoneal shunt). An alternative treatment for obstructive hydrocephalus in selected patients is the endoscopic third ventriculostomy (ETV), whereby a surgically created opening in the floor of the third ventricle allows the CSF to flow directly to the basal cisterns, thereby shortcutting any obstruction, as in aqueductal stenosis. This may or may not be appropriate based on individual anatomy. For infants, ETV is sometimes combined with choroid plexus cauterization, which reduces the amount of cerebrospinal fluid produced by the brain. The technique, known as ETV/CPC was pioneered in Uganda by neurosurgeon Ben Warf and is now in use in several U.S. hospitals.

The prognosis for individuals with schizencephaly varies depending on the size of the clefts and the degree of neurological deficit.

The diagnosis of lissencephaly is usually made at birth or soon after by ultrasound, computed tomography (CT), or magnetic resonance imaging (MRI). However, these results should be interpreted cautiously since even experienced radiologists can misdiagnose polymicrogyria, a different developmental malformation of the brain, as lissencephaly.

Before birth, complex ultrasounds performed routinely during pregnancy may indicate the presence of cerebral abnormality, but this method of diagnosis should be complemented by other methods, such as genetic studies and NMR, and the examination is not recommended as part of routine ultrasound examinations, unless family medical history or other reasons for suspecting brain malformation are present. The earliest point during gestation when it is possible to observe abnormal development of the brain surface is approximately in week 20, although ultrasound examinations in week 25–30 are more common. Up to this time, the fetal brain normally has a smooth appearance. If lissencephaly is suspected, chorionic villus sampling can test for some lissencephaly variants, but only those with a known genetic mutation.

Prenatal Diagnosis:

- Aymé, "et al." (1989) reported prenatal diagnosis of Fryns syndrome by sonography between 24 and 27 weeks.

- Manouvrier-Hanu et al. (1996) described the prenatal diagnosis of Fryns syndrome by ultrasonographic detection of diaphragmatic hernia and cystic hygroma. The diagnosis was confirmed after termination of the pregnancy. The fetus also had 2 erupted incisors; natal teeth had not been mentioned in other cases of Fryns syndrome.

Differential Diagnosis:

- McPherson et al. (1993) noted the phenotypic overlap between Fryns syndrome and the Pallister–Killian syndrome (601803), which is a dysmorphic syndrome with tissue-specific mosaicism of tetrasomy 12p.

- Veldman et al. (2002) discussed the differentiation between Fryns syndrome and Pallister–Killian syndrome, noting that differentiation is important to genetic counseling because Fryns syndrome is an autosomal recessive disorder and Pallister–Killian syndrome is usually a sporadic chromosomal aberration. However, discrimination may be difficult due to the phenotypic similarity. In fact, in some infants with 'coarse face,' acral hypoplasia, and internal anomalies, the initial diagnosis of Fryns syndrome had to be changed because mosaicism of isochromosome 12p was detected in fibroblast cultures or kidney tissue. Although congenital diaphragmatic hernia is a common finding in both syndromes, bilateral congenital diaphragmatic hernia had been reported only in patients with Fryns syndrome until the report of the patient with Pallister–Killian syndrome by Veldman et al. (2002).

- Slavotinek (2004) reviewed the phenotypes of 52 reported cases of Fryns syndrome and reevaluated the diagnostic guidelines. She concluded that congenital diaphragmatic hernia and distal limb hypoplasia are strongly suggestive of Fryns syndrome, with other diagnostically relevant findings including pulmonary hypoplasia, craniofacial dysmorphism, polyhydramnios, and orofacial clefting. Slavotinek (2004) stated that other distinctive anomalies not mentioned in previous guidelines include ventricular dilatation or hydrocephalus, agenesis of the corpus callosum, abnormalities of the aorta, dilatation of the ureters, proximal thumbs, and broad clavicles.

In some cases, the defect is linked to mutations of the EMX2, SIX3, and Collagen, type IV, alpha 1 genes. Because having a sibling with schizencephaly has been statistically shown to increase risk of the disorder, it is possible that there is a heritable genetic component to the disease.

Treatment for individuals with Dandy–Walker Syndrome generally consists of treating the associated problems, if needed.

A special tube (shunt) to reduce intracranial pressure may be placed inside the skull to control swelling. Endoscopic third ventriculostomy is also an option.

Treatment may also consist of various therapies such as occupational therapy, physiotherapy, speech therapy or specialized education. Services of a teacher of students with blindness/visual impairment may be helpful if the eyes are affected.

The spectrum of lissencephaly is only now becoming more defined as neuroimaging and genetics have provided more insights into migration disorders. There are around 20 types of lissencephaly which make up the spectrum. Other causes which have not yet been identified are likely as well.

Different systems for classifying lissencephaly exist. One major distinction is "classic" (type I) vs. "cobblestone" (type II), but some systems add additional forms that fit into neither of these categories.

Some types of lissencephaly are described below (OMIM numbers are included where available):

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

Recent research has found that Dandy–Walker syndrome often occurs in patients with PHACES syndrome.

Genetic counseling is often recommended to provide more information about fetal CPCs, to answer questions and concerns, and to outline available options such as amniocentesis or a blood test from the mother. There is a possible association between ultrasound-detected fetal CPCs and Trisomy 18. It is not correlated to the presence of Trisomy 21 (Down syndrome).

Generally the risks are very low if there are no other risk factors. If no additional abnormalities are detected by a thorough "level II" ultrasound, the likelihood the fetus has trisomy 18 is very low.

A meta-analysis of 8 studies between 1990 and 2000 with choroid plexus cysts that were identified in second-trimester (an incidence of 1.2%). The incidence of the cysts in women younger than 35 was 1% (n=1017). The study found no cases of trisomy 18 in fetuses with cysts whose mother was younger than 35. The study concluded that "there is no evidence that detection of isolated choroid plexus cyst in women who are <35 years of age increases the risk of trisomy 18".

Other factors which may have a bearing on the baby's chances of developing chromosome problems include:

- mother's age at the expected date of delivery

- the results of serum screening; XAFP triple testing or quad screening

- evidence of other "fetal findings" seen at the time of the ultrasound that may suggest a chromosome problem

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 limitation of the Spetzler-Martin Grading system is that it does not include the following factors: Patient age, hemorrhage, diffuseness of nidus, and arterial supply. In 2010 a new supplemented Spetzler-Martin system (SM-supp, Lawton-Young) was devised adding these variables to the SM system. Under this new system AVMs are classified from grades 1 - 10. It has since been determined to have greater predictive accuracy that Spetzler-Martin grades alone.

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.

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.