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.

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.

When Budd–Chiari syndrome is suspected, measurements are made of liver enzyme levels and other organ markers (creatinine, urea, electrolytes, LDH).

Budd–Chiari syndrome is most commonly diagnosed using ultrasound studies of the abdomen and retrograde angiography. Ultrasound may show obliteration of hepatic veins, thrombosis or stenosis, spiderweb vessels, large collateral vessels, or a hyperechoic cord replacing a normal vein. Computed tomography (CT) or magnetic resonance imaging (MRI) is sometimes employed although these methods are generally not as sensitive. Liver biopsy is nonspecific but sometimes necessary to differentiate between Budd–Chiari syndrome and other causes of hepatomegaly and ascites, such as galactosemia or Reye's syndrome.

Ultrasonography (US) is the first-line imaging technique for the diagnosis and follow-up of portal hypertension because it is non-invasive, low-cost and can be performed on-site.

Signs of portal hypertension on ultrasound include dilatation of the portal vein of over 13 mm in diameter, a portal flow mean velocity of less than 12 cm/s on Doppler ultrasound, porto–systemic collateral veins (patent paraumbilical vein, spleno–renal collaterals and dilated left and short gastric veins), splenomegaly and signs of cirrhosis (including nodularity of the liver surface).

The hepatic venous pressure gradient (HVPG) measurement has been accepted as the gold standard for assessing the severity of portal hypertension. Portal hypertension is defined as HVPG greater than or equal to 5 mm Hg and is considered to be clinically significant when HVPG exceeds 10 to 12 mm Hg.

The diagnosis of portopulmonary hypertension is based on hemodynamic criteria:

1. . Portal hypertension and/or liver disease (clinical diagnosis—ascites/varices/splenomegaly)

2. . Mean pulmonary artery pressure—MPAP > 25 mmHg at rest

3. . Pulmonary vascular resistance—PVR > 240 dynes s cm−5

4. . Pulmonary artery occlusion pressure— PAOP 12 mmHg where TPG = MPAP − PAOP.

The diagnosis is usually first suggested by a transthoracic echocardiogram, part of the standard pre-transplantation work-up. Echocardiogram estimated pulmonary artery systolic pressures of 40 to 50 mm Hg are used as a screening cutoff for PPH diagnosis, with a sensitivity of 100% and a specificity as high as 96%. The negative predictive value of this method is 100% but the positive predictive value is 60%. Thereafter, these patients are referred for pulmonary artery catheterization.

The limitations of echocardiography are related to the derivative nature of non-invasive PAP estimation. The measurement of PAP by echocardiogram is made using a simplified Bernoulli equation. High cardiac index and pulmonary capillary wedge pressures, however, may lead to false positives by this standard. By one institution’s evaluation, the correlation between estimated systolic PAP and directly measured PAP was poor, 0.49. For these reasons, right heart catheterization is needed to confirm the diagnosis.

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

Several studies have attempted to predict the survival of patients with Budd–Chiari syndrome. In general, nearly 2/3 of patients with Budd–Chiari are alive at 10 years. Important negative prognostic indicators include ascites, encephalopathy, elevated Child-Pugh scores, elevated prothrombin time, and altered serum levels of various substances (sodium, creatinine, albumin, and bilirubin). Survival is also highly dependent on the underlying cause of the Budd–Chiari syndrome. For example, a patient with an underlying myeloproliferative disorder may progress to acute leukemia, independently of Budd–Chiari syndrome.

Identification of AVMs requires detailed medical imaging of the organs most commonly affected by these lesions. Not all AVMs cause symptoms or are at risk of doing so, and hence there is a degree of variation between specialists as to whether such investigations would be performed, and by which modality; often, decisions on this issue are reached together with the patient.

Lung AVMs may be suspected because of the abnormal appearance of the lungs on a chest X-ray, or hypoxia (low oxygen levels) on pulse oximetry or arterial blood gas determination. Bubble contrast echocardiography (bubble echo) may be used as a screening tool to identify abnormal connections between the lung arteries and veins. This involves the injection of agitated saline into a vein, followed by ultrasound-based imaging of the heart. Normally, the lungs remove small air bubbles from the circulation, and they are therefore only seen in the right atrium and the right ventricle. If an AVM is present, bubbles appear in the left atrium and left ventricle, usually 3–10 cardiac cycles after the right side; this is slower than in heart defects, in which there are direct connections between the right and left side of the heart. A larger number of bubbles is more likely to indicate the presence of an AVM. Bubble echo is not a perfect screening tool as it can miss smaller AVMs and does not identify the site of AVMs. Often contrast-enhanced computed tomography (CT angiography) is used to identify lung lesions; this modality has a sensitivity of over 90%. It may be possible to omit contrast administration on modern CT scanners. Echocardiography is also used if there is a suspicion of pulmonary hypertension or high-output cardiac failure due to large liver lesions, sometimes followed by cardiac catheterization to measure the pressures inside the various chambers of the heart.

Liver AVMs may be suspected because of abnormal liver function tests in the blood, because the symptoms of heart failure develop, or because of jaundice or other symptoms of liver dysfunction. The most reliable initial screening test is Doppler ultrasonography of the liver; this has a very high sensitivity for identifying vascular lesions in the liver. If necessary, contrast-enhanced CT may be used to further characterize AVMs. It is extremely common to find incidental nodules on liver scans, most commonly due to focal nodular hyperplasia (FNH), as these are a hundredfold times more common in HHT compared to the general population. FNH is regarded as harmless. Generally, tumor markers and additional imaging modalities are used to differentiate between FNH and malignant tumors of the liver. Liver biopsy is discouraged in people with HHT as the risk of hemorrhage from liver AVMs may be significant. Liver scans may be useful if someone is suspected of HHT, but does not meet the criteria (see below) unless liver lesions can be demonstrated.

Brain AVMs may be detected on computed tomography angiography (CTA or CT angio) or magnetic resonance angiography (MRA); CTA is better in showing the vessels themselves, and MRA provides more detail about the relationship between an AVM and surrounding brain tissue. In general, MRI is recommended. Various types of vascular malformations may be encountered: AVMs, micro-AVMs, telangiectasias and arteriovenous fistulas. If surgery, embolization, or other treatment is contemplated (see below), cerebral angiography may be required to get sufficient detail of the vessels. This procedure carries a small risk of stroke (0.5%) and is therefore limited to specific circumstances. Recent professional guidelines recommend that all children with suspected or definite HHT undergo a brain MRI early in life to identify AVMs that can cause major complications. Others suggest that screening for cerebral AVMs is probably unnecessary in those who are not experiencing any neurological symptoms, because most lesions discovered on screening scans would not require treatment, creating undesirable conundrums.

Genetic tests are available for the "ENG", "ACVRL1" and "MADH4" mutations. Testing is not always needed for diagnosis, because the symptoms are sufficient to distinguish the disease from other diagnoses. There are situations in which testing can be particularly useful. Firstly, children and young adults with a parent with definite HHT may have limited symptoms, yet be at risk from some of the complications mentioned above; if the mutation is known in the affected parent, absence of this mutation in the child would prevent the need for screening tests. Furthermore, genetic testing may confirm the diagnosis in those with limited symptoms who otherwise would have been labeled "possible HHT" (see below).

Genetic diagnosis in HHT is difficult, as mutations occur in numerous different locations in the linked genes, without particular mutations being highly frequent (as opposed to, for instance, the ΔF508 mutation in cystic fibrosis). Sequence analysis of the involved genes is therefore the most useful approach (sensitivity 75%), followed by additional testing to detect large deletions and duplications (additional 10%). Not all mutations in these genes have been linked with disease.

Mutations in the "MADH4" gene is usually associated with juvenile polyposis, and detection of such a mutation would indicate a need to screen the patient and affected relatives for polyps and tumors of the large intestine.

Selective shunts select non-intestinal flow to be shunted to the systemic venous drainage while leaving the intestinal venous drainage to continue to pass through the liver. The most well known of this type is the splenorenal. This connects the splenic vein to the left renal vein thus reducing portal system pressure while minimizing any encephalopathy. In an H-shunt, which could be mesocaval (from the superior mesenteric vein to the inferior vena cava) or could be, portocaval (from the portal vein to the inferior vena cava) a graft, either synthetic or the preferred vein harvested from somewhere else on the patient's body, is connected between the superior mesenteric vein and the inferior vena cava. The size of this shunt will determine how selective it is.

It should be noted that with the advent of transjugular intrahepatic portosystemic shunting (TIPS), portosystemic shunts are less performed. TIPS has the advantage of being easier to perform and doesn't disrupt the liver's vascularity.

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.

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.

The diagnosis of minimal hepatic encephalopathy requires neuropsychological testing by definition. Older tests include the "numbers connecting test" A and B (measuring the speed at which one could connect randomly dispersed numbers 1–20), the "block design test" and the "digit-symbol test". In 2009 an expert panel concluded that neuropsychological test batteries aimed at measuring multiple domains of cognitive function are generally more reliable than single tests, and tend to be more strongly correlated with functional status. Both the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) and PSE-Syndrom-Test may be used for this purpose. The PSE-Syndrom-Test, developed in Germany and validated in several other European countries, incorporates older assessment tools such as the number connection test.

Hepatic microvascular dysplasia (HMD or MVD) or portal atresia is a disorder where mixing of venous blood and arterial blood in the liver occurs at the microscopic level. It occurs most commonly in certain dog breeds such as the Cairn and Yorkshire terriers although any dog breed may be at risk.

This disease may also be found in cats.

HMD is sometimes misdiagnosed as Portosystemic vascular anomaly (PSVA) or a "Liver Shunt" (portosystemic shunt). HMD can be diagnosed with an MRI, using a tracing dye in the subject's blood, and observing the flow of blood through the subject's liver and surrounding areas (stomach, intestine) for anomalies. It can also be diagnosed using a bile-acid level test; or more accurately, a "fasting-blood ammonia levels" test. Symptoms include stunted growth in the first 6–9 months, vomiting, seizures, and hydro-encephalitic episodes (from ammonia concentrating in the blood). HMD is usually treated non-surgically with antibiotics (metronidazole) and stool-softeners (lactulose).

The hepatopulmonary syndrome is suspected in any patient with known liver disease who reports dyspnea (particularly platypnea). Patients with clinically significant symptoms should undergo pulse oximetry. If the syndrome is advanced, arterial blood gasses should be measured on air.

A useful diagnostic test is contrast echocardiography. Intravenous microbubbles (> 10 micrometers in diameter) from agitated normal saline that are normally obstructed by pulmonary capillaries (normally <8 to 15 micrometers) rapidly transit the lung and appear in the left atrium of the heart within 7 heart beats. Similarly, intravenous technetium (99mTc) albumin aggregated may transit the lungs and appear in the kidney and brain. Pulmonary angiography may reveal diffusely fine or blotchy vascular configuration. The distinction has to be made with an intracardiac right-to-left shunt.

Screening among family members of people with known FH is cost-effective. Other strategies such as universal screening at the age of 16 were suggested in 2001. The latter approach may however be less cost-effective in the short term. Screening at an age lower than 16 was thought likely to lead to an unacceptably high rate of false positives.

A 2007 meta-analysis found that "the proposed strategy of screening children and parents for familial hypercholesterolaemia could have considerable impact in preventing the medical consequences of this disorder in two generations simultaneously." "The use of total cholesterol alone may best discriminate between people with and without FH between the ages of 1 to 9 years."

Screening of toddlers has been suggested, and results of a trial on 10,000 one-year-olds were published in 2016. Work was needed to find whether screening was cost-effective, and acceptable to families.

Following diagnosis, mean survival of patients with PPH is 15 months. The survival of those with cirrhosis is sharply curtailed by PPH but can be significantly extended by both medical therapy and liver transplantation, provided the patient remains eligible.

Eligibility for transplantation is generally related to mean pulmonary artery pressure (PAP). Given the fear that those PPH patients with high PAP will suffer right heart failure following the stress of post-transplant reperfusion or in the immediate perioperative period, patients are typically risk-stratified based on mean PAP. Indeed, the operation-related mortality rate is greater than 50% when pre-operative mean PAP values lie between 35 and 50 mm Hg; if mean PAP exceeds 40-45, transplantation is associated with a perioperative mortality of 70-80% (in those cases without preoperative medical therapy). Patients, then, are considered to have a high risk of perioperative death once their mean PAP exceeds 35 mm_Hg.

Survival is best inferred from published institutional experiences. At one institution, without treatment, 1-year survival was 46% and 5-year survival was 14%. With medical therapy, 1-year survival was 88% and 5-year survival was 55%. Survival at 5 years with medical therapy followed by liver transplantation was 67%. At another institution, of the 67 patients with PPH from 1652 total cirrhotics evaluated for transplant, half (34) were placed on the waiting list. Of these, 16 (48%) were transplanted at a time when 25% of all patients who underwent full evaluation received new livers, meaning the diagnosis of PPH made a patient twice as likely to be transplanted, once on the waiting list. Of those listed for transplant with PPH, 11 (33%) were eventually removed because of PPH, and 5 (15%) died on the waitlist. Of the 16 transplanted patients with PPH, 11 (69%) survived for more than a year after transplant, at a time when overall one-year survival in that center was 86.4%. The three year post-transplant survival for patients with PPH was 62.5% when it was 81.02% overall at this institution.

Routine complete blood count (CBC), basic metabolic profile, liver enzymes, and coagulation should be performed. Most experts recommend a diagnostic paracentesis be performed if the ascites is new or if the patient with ascites is being admitted to the hospital. The fluid is then reviewed for its gross appearance, protein level, albumin, and cell counts (red and white). Additional tests will be performed if indicated such as microbiological culture, Gram stain and cytopathology.

The "serum-ascites albumin gradient" (SAAG) is probably a better discriminant than older measures (transudate versus exudate) for the causes of ascites. A high gradient (> 1.1 g/dL) indicates the ascites is due to portal hypertension. A low gradient (< 1.1 g/dL) indicates ascites of non-portal hypertensive as a cause.

Ultrasound investigation is often performed prior to attempts to remove fluid from the abdomen. This may reveal the size and shape of the abdominal organs, and Doppler studies may show the direction of flow in the portal vein, as well as detecting Budd-Chiari syndrome (thrombosis of the hepatic vein) and portal vein thrombosis. Additionally, the sonographer can make an estimation of the amount of ascitic fluid, and difficult-to-drain ascites may be drained under ultrasound guidance. An abdominal CT scan is a more accurate alternate to reveal abdominal organ structure and morphology.

The diagnosis of hepatic encephalopathy can only be made in the presence of confirmed liver disease (types A and C) or a portosystemic shunt (type B), as its symptoms are similar to those encountered in other encephalopathies. To make the distinction, abnormal liver function tests and/or ultrasound suggesting liver disease are required, and ideally liver biopsy. The symptoms of hepatic encephalopathy may also arise from other conditions, such as cerebral haemorrhage and seizures (both of which are more common in chronic liver disease). A CT scan of the brain may be required to exclude haemorrhage, and if seizure activity is suspected an electroencephalograph (EEG) study may be performed. Rarer mimics of encephalopathy are meningitis, encephalitis, Wernicke's encephalopathy and Wilson's disease; these may be suspected on clinical grounds and confirmed with investigations.

The diagnosis of hepatic encephalopathy is a clinical one, once other causes for confusion or coma have been excluded; no test fully diagnoses or excludes it. Serum ammonia levels are elevated in 90% of people, but not all hyperammonaemia (high ammonia levels) is associated with encephalopathy. A CT scan of the brain usually shows no abnormality except in stage IV encephalopathy, when cerebral oedema may be visible. Other neuroimaging modalities, such as magnetic resonance imaging (MRI), are not currently regarded as useful, although they may show abnormalities. Electroencephalography shows no clear abnormalities in stage 0, even if minimal HE is present; in stages I, II and III there are triphasic waves over the frontal lobes that oscillate at 5 Hz, and in stage IV there is slow delta wave activity. However, the changes in EEG are not typical enough to be useful in distinguishing hepatic encephalopathy from other conditions.

Once the diagnosis of encephalopathy has been made, efforts are made to exclude underlying causes (such as listed above in "causes"). This requires blood tests (urea and electrolytes, full blood count, liver function tests), usually a chest X-ray, and urinalysis. If there is ascites, diagnostic paracentesis (removal of a fluid sample with a needle) may be required to identify spontaneous bacterial peritonitis (SBP).

Ascites exists in three grades:

- Grade 1: mild, only visible on ultrasound and CT

- Grade 2: detectable with flank bulging and shifting dullness

- Grade 3: directly visible, confirmed with the fluid wave/thrill test

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.

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.

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.

Bronchopulmonary sequestration (BPS) is a rare congenital malformation of the lower respiratory tract.

It consists of a nonfunctioning mass of normal lung tissue that lacks normal communication with the tracheobronchial tree, and that receives its arterial blood supply from the systemic circulation.

BPS is estimated to comprise 0.15 to 6.4 percent of all congenital pulmonary malformations, making it an extremely rare disorder.

Sequestrations are classified anatomically.

Intralobar sequestration (ILS) in which the lesion is located within a normal lobe and lacks its own visceral pleura.

Extralobar sequestration (ELS) in which the mass is located outside the normal lung and has its own visceral pleura

The blood supply of 75% of pulmonary sequestrations is derived from the thoracic or abdominal aorta.

The remaining 25% of sequestrations receive their blood flow from the subclavian, intercostal, pulmonary, pericardiophrenic, innominate, internal mammary, celiac, splenic, or renal arteries.