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

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.

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.

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.

Symptoms of congenital PSS usually appear by six months of age and include failure to gain weight, vomiting, and signs of hepatic encephalopathy (a condition where toxins normally removed by the liver accumulate in the blood and impair the function of brain cells) such as seizures, depression, tremors, drooling, and head pressing. Urate bladder stones may form because of increased amounts of uric acid in circulation and excreted by the kidneys. Initial diagnosis of PSS is through laboratory bloodwork showing either elevated serum bile acids after eating or elevation of fasting blood ammonia levels, which has been shown to have a higher sensitivity and specificity than the bile acids test.

Various diagnostic imaging techniques are used to demonstrate PSS. Ultrasonography is a rapid, convenient, non-invasive, and accurate method for diagnosis of PSS. Ultrasonographic diagnosis of congenital PSS depends on finding an anomalous vessel either in the liver or just caudal to the liver in the dorsal abdomen, usually draining into the caudal vena cava. Ultrasonography can also be used to estimate hepatic volume and vascularity, and to identify related lesions affecting other abdominal structures, such as urinary calculi. Computed tomography (CT) may be considered when ultrasound expertise is lacking or ultrasonography is considered sub-optimal (e.g. because of the conformation of the patient). Control of respiration and careful timing of CT acquisition after contrast injection is necessary for optimal depiction of PSS. Rectal portal scintigraphy using technetium pertechnetate, a technique of imaging involving detection of gamma rays emitted by radionuclides absorbed through the rectum and into the bloodstream, demonstrates the blood vessel bypassing the liver. In certain institutions, scintigraphy is the preferred diagnostic technique, but this leaves the patient radioactive for 24h, which may be inconvenient depending on nursing needs. Portal venography is the definitive method for demonstrating PSS, but is invasive, hence it is best reserved for animals with a known shunt or those considered highly likely to have a shunt that was not detectable by ultrasonography.

In regards to the diagnosis of pulmonary atresia the body requires oxygenated blood for survival. pulmonary atresia is not threatening to a developing fetus however, because the mother's placenta provides the needed oxygen since the baby's lungs are not yet functional. Once the baby is born its lungs must now provide the oxygen needed for survival, but with pulmonary atresia there is no opening on the pulmonary valve for blood to get to the lungs and become oxygenated. Due to this, the newborn baby is blue in color and pulmonary atresia can usually be diagnosed within hours or minutes after birth.

The diagnosis of pulmonary atresia can be done via the following exams/methods: an echocardiogram, chest x-ray, EKG and an exam to measure the amount of in the body.

Abdominal ultrasound is of some benefit, but not diagnostic. Features that suggest posterior urethral valves are bilateral hydronephrosis, a thickened bladder wall with thickened smooth muscle trabeculations, and bladder diverticula.

Voiding cystourethrogram (VCUG) is more specific for the diagnosis. Normal "plicae circularis" are variable in appearance and often not seen on normal VCUGs. PUV on voiding cystourethrogram is characterized by an abrupt tapering of urethral caliber near the verumontanum, with the specific level depending on the developmental variant. Vesicoureteral reflux is also seen in over 50% of cases. Very often the posterior urethra maybe dilated thus making the abrupt narrowing more obvious. the bladder wall may show trabeculations or sacculations or even diverticuli.

Diagnosis can also be made by cystoscopy, where a small camera is inserted into the urethra for direct visualization of the posteriorly positioned valve. A limitation of this technique is that posterior valve tissue is translucent and can be pushed against the wall of the urethra by inflowing irrigation fluid, making it difficult to visualize. Cystoscopy may also demonstrate the bladder changes.

Centers in Europe and Japan have also had excellent results with cystosonography, although it has not been approved for use in the United States yet.

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.

Surgical treatment is best, when it can be performed. Pressure within the portal vein is measured as the shunt is closed, and it must be kept below 20 cm HO or else portal hypertension will ensue. Methods of shunt attenuation should aim to slowly occlude the vessel over several weeks to months in order to avoid complications associated with portal hypertension. These methods include ameroid ring constrictors, cellophane banding, intravascular or percutaneous silicone hydraulic occluders. The most common methods of attenuation used by veterinarians are ameroid ring constrictors and cellophane banding. Both methods have reportedly good outcomes in both cats and dogs, although the true composition of readily sourced cellophane has been found to be made from plastics (inert) and not cellulose (stimulates a fibrous reaction). Recently, a commercial supplier of regenerated cellulose based cellophane for veterinarians has been established for use of cellophane banding for portosystemic shunts in dogs and cats. Complete closure of extrahepatic shunts results in a very low recurrence rate, while incomplete closure results in a recurrence rate of about 50 percent. However, not all dogs with extrahepatic shunts tolerate complete closure (16 to 68 percent). Intrahepatic shunts are much more difficult to surgically correct than extrahepatic shunts due to their hidden nature, large vessel size, and greater tendency toward portal hypertension when completely closed. When surgery is not an option, PSS is treated as are other forms of liver failure. Dietary protein restriction is helpful to lessen signs of hepatic encephalopathy, and antibiotics such as neomycin or metronidazole and other medicines such as lactulose can reduce ammonia production and absorption in the intestines. The prognosis is guarded for any form of PSS.

The prognosis for pulmonary atresia varies for every child, if the condition is left uncorrected it may be fatal, but the prognosis has greatly improved over the years for those with pulmonary atresia. Some factors that affect how well the child does include how well the heart is beating, and the condition of the blood vessels that supply the heart. Most cases of pulmonary atresia can be helped with surgery, if the patient's right ventricle is exceptionally small, many surgeries will be needed in order to help stimulate normal circulation of blood to the heart.If uncorrected, babies with this type of congenital heart disease may only survive for the first few days of life. Many children with pulmonary atresia will go on to lead normal lives, though complications such as endocarditis, stroke and seizures are possible.

The radiocephalic arteriovenous fistula (RC-AVF) is a shortcut between cephalic vein and radial artery at the wrist. It is the recommended first choice for hemodialysis access. Possible underlying causes for failure are stenosis and thrombosis especially in diabetics and those with low blood flow such as due to narrow vessels, arteriosclerosis and advanced age. Reported patency of fistulae after 1 year is about 62.5%.

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."

For proper diagnosis of situs ambiguous, cardiac and non-cardiac features must be evaluated. Diagnostic criteria for atrial isomerism includes observation of symmetry of thoracic visceral organs upon echocardiogram, arrhythmia upon electrocardiogram, and chest x-ray for confirmation of the heart's location across the left-right axis. In addition, a series of gastrointestinal tests can be conducted for observation of intestinal malrotation, as well as a scan of the liver and spleen for biliary function.

l-TGA can sometimes be diagnosed in utero with an ultrasound after 18 weeks gestation. However, many cases of simple l-TGA are "accidentally" diagnosed in adulthood, during diagnosis or treatment of other conditions.

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.

Although its cause is poorly understood, situs ambiguous has been linked to family history of malformations and maternal cocaine use, suggesting both genetic and environmental factors play a role. Several genes in the TGF-beta pathway, which controls left-right patterning of viseral organs across the body axis, have been indicated in sporadic and familial cases of atrial isomerism.

There does not appear to be a screening method for prevention of heterotaxy syndrome. However, genetic testing in family members that display atrial isomerism or other cardiac malformations may help to discern risk for additional family members, especially in X-linked causes of heterotaxy syndrome.

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.

Congenital heart defects are now diagnosed with echocardiography, which is quick, involves no radiation, is very specific, and can be done prenatally.

Before more sophisticated techniques became available, chest x-ray was the definitive method of diagnosis. The abnormal "coeur-en-sabot" (boot-like) appearance of a heart with tetralogy of Fallot is classically visible via chest x-ray, although most infants with tetralogy may not show this finding. Absence of interstitial lung markings secondary to pulmonary oligaemia are another classic finding in tetralogy, as is the pulmonary bay sign.

The procedure was invented by doctors James Cimino and M. J. Brescia in 1966. Before the Cimino fistula was invented, access was through a Scribner shunt, which consisted of a Teflon tube with a needle at each end. Between treatments, the needles were left in place and the tube allowed blood flow to reduce clotting. But Scribner shunts lasted only a few days to weeks. Frustrated by this limitation, James E. Cimino recalled his days as a phlebotomist (blood drawer) at New York City's Bellevue Hospital in the 1950s when Korean War veterans showed up with fistulas caused by trauma. Cimino recognized that these fistulas did not cause the patients harm and were easy places to get repeated blood samples. He convinced surgeon Kenneth Appell to create some in patients with chronic kidney failure and the result was a complete success. Scribner shunts were quickly replaced with Cimino fistulas, and they remain the most effective, longest-lasting method for long-term access to patients' blood for hemodialysis today.

Hypoplastic left heart syndrome can be diagnosed prenatally or after birth via echocardiography. Typical findings include a small left ventricle and aorta, abnormalities of the mitral and aortic valves, retrograde flow in the transverse arch of the aorta, and left-to-right flow between the atria. It is often recognized during the second trimester of pregnancy, between 18 and 24 weeks' gestation.

If suspected antenatally, a consultation with a paediatric surgeon/ paediatric urologist maybe indicated to evaluate the risk and consider treatment options.

Treatment is by endoscopic valve ablation. Fetal surgery is a high risk procedure reserved for cases with severe oligohydramnios, to try to limit the associated lung underdevelopment, or pulmonary hypoplasia, that is seen at birth in these patients. The risks of fetal surgery are significant and include limb entrapment, abdominal injury, and fetal or maternal death. Specific procedures for "in utero" intervention include infusions of amniotic fluid, serial bladder aspiration, and creating a connection between the amniotic sac and the fetal bladder, or vesicoamniotic shunt.

There are three specific endoscopic treatments of posterior urethral valves:

- Vesicostomy followed by valve ablation - a stoma, or hole, is made in the urinary bladder, also known as "low diversion", after which the valve is ablated and the stoma is closed.

- Pyelostomy followed by valve ablation - stoma is made in the pelvis of the kidney as a slightly "high diversion", after which the valve is ablated and the stoma is closed

- Primary (transurethral) valve ablation - the valve is removed through the urethra without creation of a stoma

The standard treatment is primary (transurethral) ablation of the valves. Urinary diversion is used in selected cases, and its benefit is disputed.

Following surgery, the follow-up in patients with posterior urethral valve syndrome is long term, and often requires a multidisciplinary effort between paediatric surgeons/ paediatric urologists, pulmonologists, neonatologists, radiologists and the family of the patient. Care must be taken to promote proper bladder compliance and renal function, as well as to monitor and treat the significant lung underdevelopment that can accompany the disorder. Definitive treatment may also be indicated for the vesico-ureteral reflux.

d-TGA can sometimes be diagnosed in utero with an ultrasound after 18 weeks gestation. However, if it is not diagnosed in utero, cyanosis of the newborn (blue baby) should immediately indicate that there is a problem with the cardiovascular system. Normally, the lungs are examined first, then the heart is examined if there are no apparent problems with the lungs. These examinations are typically performed using ultrasound, known as an echocardiogram when performed on the heart. Chest x-rays and electrocardiograms (EKG) may also be used in reaching or confirming a diagnosis; however, an x-ray may appear normal immediately following birth. If d-TGA is accompanied by both a VSD and pulmonary stenosis, a systolic murmur will be present.

On the rare occasion (when there is a large VSD with no significant left ventricular outflow tract obstruction), initial symptoms may go unnoticed, resulting in the infant being discharged without treatment in the event of a hospital or birthing center birth, or a delay in bringing the infant for diagnosis in the event of a home birth. On these occasions, a layperson is likely not to recognize symptoms until the infant is experiencing moderate to serious congestive heart failure (CHF) as a result of the heart working harder in a attempt to increase oxygen flow to the body; this overworking of the heart muscle eventually leads to hypertrophy and may result in cardiac arrest if left untreated.

The original criteria for IIH were described by Dandy in 1937.

They were modified by Smith in 1985 to become the "modified Dandy criteria". Smith included the use of more advanced imaging: Dandy had required ventriculography, but Smith replaced this with computed tomography. In a 2001 paper, Digre and Corbett amended Dandy's criteria further. They added the requirement that the patient is awake and alert, as coma precludes adequate neurological assessment, and require exclusion of venous sinus thrombosis as an underlying cause. Furthermore, they added the requirement that no other cause for the raised ICP is found.

In a 2002 review, Friedman and Jacobson propose an alternative set of criteria, derived from Smith's. These require the absence of symptoms that could not be explained by a diagnosis of IIH, but do not require the actual presence of any symptoms (such as headache) attributable to IIH. These criteria also require that the lumbar puncture is performed with patient lying sideways, as a lumbar puncture performed in the upright sitting position can lead to artificially high pressure measurements. Friedman and Jacobson also do not insist on MR venography for every patient; rather, this is only required in atypical cases (see "diagnosis" above).

With simple d-TGA, if the foramen ovale and ductus arteriosus are allowed to close naturally, the newborn will likely not survive long enough to receive corrective surgery. With complex d-TGA, the infant will fail to thrive and is unlikely to survive longer than a year if corrective surgery is not performed. In most cases, the patient's condition will deteriorate to the point of inoperability if the defect is not corrected in the first year.

While the foramen ovale and ductus arteriosus are open after birth, some mixing of red and blue blood occurs allowing a small amount of oxygen to be delivered to the body; if ASD, VSD, PFO, and/or PDA are present, this will allow a higher amount of the red and blue blood to be mixed, therefore delivering more oxygen to the body, but can complicate and lengthen the corrective surgery and/or be symptomatic.

Modern repair procedures within the ideal timeframe and without additional complications have a very high success rate.

Neuroimaging, usually with computed tomography (CT/CAT) or magnetic resonance imaging (MRI), is used to exclude any mass lesions. In IIH these scans typically appear to be normal, although small or slit-like ventricles, dilatation and buckling of the optic nerve sheaths and "empty sella sign" (flattening of the pituitary gland due to increased pressure) and enlargement of Meckel's caves may be seen.

An MR venogram is also performed in most cases to exclude the possibility of venous sinus stenosis/obstruction or cerebral venous sinus thrombosis. A contrast-enhanced MRV (ATECO) scan has a high detection rate for abnormal transverse sinus stenoses. These stenoses can be more adequately identified and assessed with catheter cerebral venography and manometry. Buckling of the bilateral optic nerves with increased perineural fluid is also often noted on MRI imaging.

Lumbar puncture is performed to measure the opening pressure, as well as to obtain cerebrospinal fluid (CSF) to exclude alternative diagnoses. If the opening pressure is increased, CSF may be removed for transient relief (see below). The CSF is examined for abnormal cells, infections, antibody levels, the glucose level, and protein levels. By definition, all of these are within their normal limits in IIH. Occasionally, the CSF pressure measurement may be normal despite very suggestive symptoms. This may be attributable to the fact that CSF pressure may fluctuate over the course of the normal day. If the suspicion of problems remains high, it may be necessary to perform more long-term monitoring of the ICP by a pressure catheter.