Prostacyclin (prostaglandin I) is commonly considered the most effective treatment for PAH. Epoprostenol (synthetic prostacyclin) is given via continuous infusion that requires a semi-permanent central venous catheter. This delivery system can cause sepsis and thrombosis. Prostacyclin is unstable, and therefore has to be kept on ice during administration. Since it has a half-life of 3 to 5 minutes, the infusion has to be continuous, and interruption can be fatal. Other prostanoids have therefore been developed. Treprostinil can be given intravenously or subcutaneously, but the subcutaneous form can be very painful. An increased risk of sepsis with intravenous Remodulin has been reported by the CDC. Iloprost is also used in Europe intravenously and has a longer half life. Iloprost was the only inhaled form of prostacyclin approved for use in the US and Europe, until the inhaled form of treprostinil was approved by the FDA in July 2009.

The dual (ET and ET) endothelin receptor antagonist bosentan was approved in 2001. Sitaxentan (Thelin) was approved for use in Canada, Australia, and the European Union, but not in the United States. In 2010, Pfizer withdrew Thelin worldwide because of fatal liver complications. A similar drug, ambrisentan is marketed as Letairis in the U.S. by Gilead Sciences.

Standard medical treatment consists of anticoagulants (blood thinners), diuretics, and oxygen. Lifelong anticoagulation is recommended, even after PEA. Routine inferior vena cava filter placement is not recommended.

In patients with non-operable CTEPH or persistent/recurrent PH after PEA, there is evidence for benefit from pulmonary vasodilator drug treatment. The microvascular disease component in CTEPH has provided the rationale for off-label use of drugs approved for PAH. Currently, only riociguat (a stimulator of soluble guanylate cyclase) is approved for treatment of adults with inoperable CTEPH or persistent or recurrent CTEPH after surgical treatment. Other drug trials are ongoing in patients with inoperable CTEPH, with macitentan recently proving efficacy and safety in MERIT

The treatment for cor pulmonale can include the following: antibiotics, expectorants, oxygen therapy, diuretics, digitalis, vasodilators, and anticoagulants. Some studies have indicated that Shenmai injection with conventional treatment is safe and effective for cor pulmonale (chronic).

Treatment requires diuretics (to decrease strain on the heart). Oxygen is often required to resolve the shortness of breath. Additionally, oxygen to the lungs also helps relax the blood vessels and eases right heart failure. When wheezing is present, the majority of individuals require a bronchodilator. A variety of drugs have been developed to relax the blood vessels in the lung, calcium channel blockers are used but only work in few cases and according to NICE are not recommended for use at all.

Anticoagulants are used when venous thromboembolism is present. Venesection is used in severe secondary polycythaemia (because of hypoxia), which improves symptoms though survival rate has not been proven to increase.Finally, transplantation of single/double lung in extreme cases of cor pulmonale is also an option.

Decision making for patients with CTEPH can be complex and needs to be managed by CTEPH teams in expert centres. CTEPH teams comprise cardiologists and pulmonologists with specialist PH training, radiologists, experienced PEA surgeons with a significant caseload of CTEPH patients per year and physicians with percutaneous interventional expertise. Currently, there are three recognised targeted treatment options available: pulmonary endarterectomy (PEA), balloon pulmonary angioplasty (BPA) and pulmonary vasodilator drug treatment for inoperable patients.

Specialist imaging using either magnetic resonance or invasive PA is necessary to determine risks and benefits of interventional treatment with PEA or BPA.

Anticoagulant therapy is the mainstay of treatment. Acutely, supportive treatments, such as oxygen or analgesia, may be required. People are often admitted to hospital in the early stages of treatment, and tend to remain under inpatient care until the INR has reached therapeutic levels. Increasingly, however, low-risk cases are managed at home in a fashion already common in the treatment of DVT. Evidence to support one approach versus the other is weak.

Usually, anticoagulant therapy is the mainstay of treatment. Unfractionated heparin (UFH), low molecular weight heparin (LMWH), or fondaparinux is administered initially, while warfarin, acenocoumarol, or phenprocoumon therapy is commenced (this may take several days, usually while the patient is in the hospital). LMWH may reduce bleeding among people with pulmonary embolism as compared to UFH according to a systematic review of randomized controlled trials by the Cochrane Collaboration. According to the same review, LMWH reduced the incidence of recurrent thrombotic complications and reduced thrombus size when compared to heparin. There was no difference in overall mortality between participants treated with LMWH and those treated with unfractionated heparin.

Warfarin therapy often requires a frequent dose adjustment and monitoring of the international normalized ratio (INR). In PE, INRs between 2.0 and 3.0 are generally considered ideal. If another episode of PE occurs under warfarin treatment, the INR window may be increased to e.g. 2.5–3.5 (unless there are contraindications) or anticoagulation may be changed to a different anticoagulant e.g. LMWH.

In patients with an underlying malignancy, therapy with a course of LMWH is favored over warfarin; it is continued for six months, at which point a decision should be reached whether ongoing treatment is required.

Similarly, pregnant women are often maintained on low molecular weight heparin until at least six weeks after delivery to avoid the known teratogenic effects of warfarin, especially in the early stages of pregnancy.

Warfarin therapy is usually continued for 3–6 months, or "lifelong" if there have been previous DVTs or PEs, or none of the usual risk factors is present. An abnormal D-dimer level at the end of treatment might signal the need for continued treatment among patients with a first unprovoked pulmonary embolus. For those with small PEs (known as subsegmental PEs) the effects of anticoagulation is unknown as it has not been properly studied as of 2014.

It is sometimes treated with surgery, which involves rerouting blood from the right atrium into the left atrium with a patch or use of the Warden procedure. However, interest is increasing in catheter-based interventional approaches, as well as medical therapy for less severe cases.

In general, the treatment of PPH is derived from the treatment of pulmonary hypertension. The best treatment available is the combination of medical therapy and liver transplantation.

The ideal treatment for PPH management is that which can achieve pulmonary vasodilatation and smooth muscle relaxation without exacerbating systemic hypotension. Most of the therapies for PPH have been adapted from the primary pulmonary hypertension literature. Calcium channel blockers, b-blockers and nitrates have all been used – but the most potent and widely used aids are prostaglandin (and prostacyclin) analogs, phosphodiesterase inhibitors, nitric oxide and, most recently, endothelin receptor antagonists and agents capable of reversing the remodeling of pulmonary vasculature.

Inhaled nitric oxide vasodilates, decreasing pulmonary arterial pressure (PAP) and pulmonary vascular resistance (PVR) without affecting systemic artery pressure because it is rapidly inactivated by hemoglobin, and improves oxygenation by redistributing pulmonary blood flow to ventilated areas of lung. Inhaled nitric oxide has been used successfully to bridge patients through liver transplantation and the immediate perioperative period, but there are two significant drawbacks: it requires intubation and cannot be used for long periods of time due to methemoglobinemia.

Prostaglandin PGE1 (Alprostadil) binds G-protein linked cell surface receptors that activate adenylate cyclase to relax vascular smooth muscle. Prostacyclin – PGI2, an arachadonic acid derived lipid mediator (Epoprostenol, Flolan, Treprostenil) – is a vasodilator and, at the same time, the most potent inhibitor of platelet aggregation. More importantly, PGI2 (and not nitrous oxide) is also associated with an improvement in splanchnic perfusion and oxygenation. Epoprostenol and ilioprost (a more stable, longer acting variation) can and does successfully bridge for patients to transplant. Epoprostenol therapy can lower PAP by 29-46% and PVR by 21-71%., Ilioprost shows no evidence of generating tolerance, increases cardiac output and improves gas exchange while lowering PAP and PVR. A subset of patients does not respond to any therapy, likely having fixed vascular anatomic changes.

Phosphodiesterase inhibitors (PDE-i) have been employed with excellent results. It has been shown to reduce mean PAP by as much as 50%, though it prolongs bleeding time by inhibiting collagen-induced platelet aggregation. Another drug, Milrinone, a Type 3 PDE-i increases vascular smooth muscle adenosine-3,5-cyclic monophosphate concentrations to cause selective pulmonary vasodilation. Also, by causing the buildup of cAMP in the myocardium, Milrinone increases contractile force, heart rate and the extent of relaxation.

The newest generation in PPH pharmacy shows great promise. Bosentan is a nonspecific endothelin-receptor antagonist capable of neutralizing the most identifiable cirrhosis associated vasoconstrictor, safely and efficaciously improving oxygenation and PVR, especially in conjunction with sildenafil. Finally, where the high pressures and pulmonary tree irritations of PPH cause a medial thickening of the vessels (smooth muscle migration and hyperplasia), one can remove the cause –control the pressure, transplant the liver – yet those morphological changes persist, sometimes necessitating lung transplantation. Imatinib, designed to treat chronic myeloid leukemia, has been shown to reverse the pulmonary remodeling associated with PPH.

Neonates without adverse symptoms may simply be monitored as outpatients, while symptomatic PDA can be treated with both surgical and non-surgical methods. Surgically, the DA may be closed by ligation (though support in premature infants is mixed), either manually tied shut, or with intravascular coils or plugs that leads to formation of a thrombus in the DA.

Devices developed by Franz Freudenthal block the blood vessel with woven structures of nitinol wire.

Because prostaglandin E2 is responsible for keeping the DA open, NSAIDS (which can inhibit prostaglandin synthesis) such as indomethacin or a special form of ibuprofen have been used to initiate PDA closure. Recent findings from a systematic review concluded that, for closure of a PDA in preterm and/or low birth weight infants, ibuprofen is as effective as Indomethacin. It also causes fewer side effects (such as transient renal insufficiency) and reduces the risk of necrotising enterocolitis. Another recent review showed that paracetamol may be effective for closure of a PDA in preterm infants.

More recently, PDAs can be closed by percutaneous interventional method (avoiding open heart surgery). A platinum coil can be deployed via a catheter through the femoral vein or femoral artery, which induces thrombosis (coil embolization). Alternatively, a PDA occluder device , composed of nitinol mesh, is deployed from the pulmonary artery through the PDA.

Some evidence suggests that indomethacin administration on the first day of life to all preterm infants reduces the risk of developing a PDA and the complications associated with PDA. Indomethacin treatment in premature infants also may reduce the need for surgical intervention.

When PGE is administered to a newborn, it prevents the ductus arteriosus from closing, therefore providing an additional shunt through which to provide the systemic circulation with a higher level of oxygen.

Antibiotics may be administered preventatively. However, due to the physical strain caused by uncorrected d-TGA, as well as the potential for introduction of bacteria via arterial and central lines, infection is not uncommon in pre-operative patients.

Diuretics aid in flushing excess fluid from the body, thereby easing strain on the heart.

Analgesics normally are not used pre-operatively, but they may be used in certain cases. They are occasionally used partially for their sedative effects.

Cardiac glycosides are used to maintain proper heart rhythm while increasing the strength of each contraction.

Sedatives may be used palliatively to prevent a young child from thrashing about or pulling out any of their lines.

The treatment of pulmonary atresia consists of: an IV medication called prostaglandin E1, which is used for treatment of pulmonary atresia, as it stops the ductus arteriosus from closing, allowing mixing of the pulmonary and systemic circulations, but prostaglandin E1 can be dangerous as it can cause apnea. Another example of preliminary treatment is heart catheterization to evaluate the defect or defects of the heart; this procedure is much more invasive. Ultimately, however, the individual will need to have a series of surgeries to improve the blood flow permanently. The first surgery will likely be performed shortly after birth. A shunt can be created between the aorta and the pulmonary artery to help increase blood flow to the lungs. As the child grows, so does the heart and the shunt may need to be revised in order to meet the body's requirements.

The type of surgery recommended depends on the size of the right ventricle and the pulmonary artery, if the right ventricle is small and unable to act as a pump, the surgery performed would be the Fontan procedure. In this three-stage procedure, the right atrium is disconnected from the pulmonary circulation. The systemic venous return goes directly to the lungs, by-passing the heart.Very young children with elevated pulmonary vascular resistance may not able to undergo the Fontan procedure. Cardiac catheterization may be done to determine the resistance before going ahead with the surgery.

The infant will continue to see a cardiologist on a regular basis. Although these appointments are required less frequently as time goes on, they will continue throughout the lifetime of the individual, and may increase in the event of complications or as the individual approaches middle age.

The cardiology exam may include an echocardiogram, EKG, and/or cardiac stress test in addition to consultation.

Additionally, some individuals may require ongoing medication therapy at home, which may include diuretics (such as furosemide or spironolactone), analgesics (such as paracetamol), cardiac glycosides (such as digoxin), anticoagulants (such as heparin or aspirin), or other medications. If the individual has undergone stenting, an anticoagulant will be a necessity to prevent build-up around the stent(s), as the body will perceive the foreign body as a wound and attempt to heal it.

Some patients who had alternate corrective surgery, such as the Mustard or Senning procedure, may have issues with SA and VA nodal transmissions in later life. Typical symptoms include palpitations and problems with low heart rates. This is commonly solved with a Pacemaker unit, providing scar tissue from the original operation does not block its functionality.

More recently, ACE inhibitors have been prescribed to patients in the hope of relieving stress on the heart.

In treating pulmonary insufficiency, it should be determined if pulmonary hypertension is causing the problem to therefore begin the most appropriate therapy as soon as possible (primary pulmonary hypertension or secondary pulmonary hypertension due to thromboembolism). Furthermore, pulmonary insufficiency is generally treated by addressing the underlying condition, in certain cases, the pulmonary valve may be surgically replaced.

For newborns with transposition, prostaglandins can be given to keep the ductus arteriosus open which allows mixing of the otherwise isolated pulmonary and systemic circuits. Thus oxygenated blood that recirculates back to the lungs can mix with blood that circulates throughout the body. The arterial switch operation is the definitive treatment for dextro- transposition. Rarely the arterial switch is not feasible due to particular coronary artery anatomy and an atrial switch operation is preferred.

Without life-prolonging interventions, HLHS is fatal, but with intervention, an infant may survive. A cardiothoracic surgeon may perform a series of operations or a full heart transplant. While surgical intervention has emerged as the standard of care in the United States, other national health systems, notably in France, approach diagnosis of HLHS in a more conservative manner, with an emphasis on termination of pregnancy or compassionate care after delivery.

Before surgery, the ductus must be kept open to allow blood-flow using medication containing prostaglandin. Air with less oxygen than normal is used for infants with hypoplastic left heart syndrome. These low oxygen levels increases the pulmonary vascular resistance (PVR) and thus improve blood flow to the rest of the body, due to the greater pressure difference between the lungs and body. Achieving oxygen levels below atmosphere requires the use of inhaled nitrogen. Nitric oxide is a potent pulmonary vasodilator, and thus reduces PVR and improves venous return. Any factor that increases PVR will impede right sided flow.

Treatment is with neonatal surgical repair, with the objective of restoring a normal pattern of blood flow. The surgery is open heart, and the patient will be placed on cardiopulmonary bypass to allow the surgeon to work on a still heart. The heart is opened and the ventricular septal defect is closed with a patch. The pulmonary arteries are then detached from the common artery (truncus arteriosus) and connected to the right ventricle using a tube (a conduit or tunnel). The common artery, now separated from the pulmonary circulation, functions as the aorta with the truncal valve operating as the aortic valve. Most babies survive this surgical repair, but may require further surgery as they grow up. For example, the conduit does not grow with the child and may need to be replaced as the child grows. Furthermore, the truncal valve is often abnormal and may require future surgery to improve its function.

There have been cases where the condition has been diagnosed at birth and surgical intervention is an option. A number of these cases have survived well into adulthood.

Tet spells may be treated with beta-blockers such as propranolol, but acute episodes require rapid intervention with morphine or intranasal fentanyl to reduce ventilatory drive, a vasopressor such as phenylephrine, or norepinephrine to increase systemic vascular resistance, and IV fluids for volume expansion.

Oxygen (100%) may be effective in treating spells because it is a potent pulmonary vasodilator and systemic vasoconstrictor. This allows more blood flow to the lungs by decreasing shunting of deoxygenated blood from the right to left ventricle through the VSD. There are also simple procedures such as squatting and the knee chest position which increase systemic vascular resistance and decrease right-to-left shunting of deoxygenated blood into the systemic circulation.

In terms of treatment for pulmonary valve stenosis, valve replacement or surgical repair (depending upon whether the stenosis is in the valve or vessel) may be indicated. If the valve stenosis is of congenital origin, balloon valvuloplasty is another option, depending on the case.

Valves made from animal or human tissue (are used for valve replacement), in adults metal valves can be used.

In TAPVC without obstruction, surgical redirection can be performed within the first month of life. The operation is performed under general anesthesia. The four pulmonary veins are reconnected to the left atrium, and any associated heart defects such as atrial septal defect, ventricular septal defect, patent foramen ovale, and/or patent ductus arteriosus are surgically closed. With obstruction, surgery should be undertaken emergently. PGE1 should be given because a patent ductus arteriosus allows oxygenated blood to go from the circulation of the right heart to the systemic circulation.

To treat Lutembacher's syndrome, the underlying causes of the disorder must first be treated: mitral stenosis and atrial septal defect. Lutembacher's syndrome is usually treated surgically with treatments such as:

- percutaneous transcatheter therapy for MS

- Device closure of ASD

Percutaneous transcatheter treatment for the MS can include transcatheter therapies of such as balloon valuloplasty.

Simple l-TGA has a very good prognosis, with many individuals being asymptomatic and not requiring surgical correction.

In a number of cases, the (technically challenging) "double switch operation" has been successfully performed to restore the normal blood flow through the ventricles.

Surgical operations to assist with hypoplastic left heart are complex and need to be individualized for each patient. A cardiologist must assess all medical and surgical options on a case-by-case basis.

Currently, infants undergo either the staged reconstructive surgery (Norwood or Sano procedure within a few days of birth, Glenn or "Hemi-Fontan procedure" at 3 to 6 months of age, and the Fontan procedure at 1 1/2 to 5 years of age) or cardiac transplantation. Current expectations are that 70% of those with HLHS will reach adulthood. Many studies show that the higher the volume (number of surgeries performed) at a hospital, the lower the mortality (death) rate. Factors that increase an infant's risk include lower birth weight, additional congenital anomalies, a genetic syndrome or those with a highly restrictive atrial septum.) For patients without these additional risk factors, 5 year survival now approaches 80%. Further, studies show that about 50% of those children who survived surgery in the early development of staged reconstruction have developmental delay or need special education; about 25% of these surgical survivors have severe disabilities. There is growing evidence that while the incidence of developmental and behavioral disabilities continues to be higher than that in the general population, children operated upon in the more current era have shown significantly better neurological outcomes. An alternative to the traditional Norwood is the Hybrid procedure.

Some physicians offer "compassionate care", instead of the surgeries, which results in the child's death, usually within 2 weeks of birth. Compassionate care is overseen by a physician, and may be carried out either in the hospital or at home. However, due to the vast improvement of surgical intervention, with many hospitals achieving over 90% survival, there is debate on whether or not "compassionate care" should still be offered to families. A study in 2003 concluded that a selection of physicians who are experts in the care of children with HLHS were evenly split when asked what they would do if their own children were born with HLHS, with 1/3 stating that they would choose surgery, 1/3 stating that they would choose palliative (compassionate) treatment without surgery, and 1/3 stating that they are uncertain which choice they would make.

The three-stage procedure is a palliative procedure (not a cure), as the child's circulation is made to work with only two of the heart's four chambers.

Treatment is aimed at controlling symptoms and improving the interrupted blood flow to the affected area of the body.

Medications include:

- Antithrombotic medication. These are commonly given because thromboembolism is the major cause of arterial embolism. Examples are:

- Anticoagulants (such as warfarin or heparin) and antiplatelet medication (such as aspirin, ticlopidine, and clopidogrel) can prevent new clots from forming

- Thrombolytics (such as streptokinase) can dissolve clots

- Painkillers given intravenously

- Vasodilators to relax and dilate blood vessels.

Appropriate drug treatments successfully produces thrombolysis and removal of the clot in 50% to 80% of all cases.

Antithrombotic agents may be administered directly onto the clot in the vessel using a flexible catheter ("intra-arterial thrombolysis"). Intra-arterial thrombolysis reduces thromboembolic occlusion by 95% in 50% of cases, and restores adequate blood flow in 50% to 80% of cases.

Surgical procedures include:

- Arterial bypass surgery to create another source of blood supply

- Embolectomy, to remove the embolus, with various techniques available:

- Thromboaspiration

- Angioplasty with balloon catheterization with or without implanting a stent Balloon catheterization or open embolectomy surgery reduces mortality by nearly 50% and the need for limb amputation by approximately 35%.

- Embolectomy by open surgery on the artery

If extensive necrosis and gangrene has set in an arm or leg, the limb may have to be amputated. Limb amputation is in itself usually remarkably well tolerated, but is associated with a substantial mortality (~50%), primarily because of the severity of the diseases in patients where it is indicated.