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.

Each of the symptoms of situs ambiguous must be managed with appropriate treatment dependent upon the organ system involved. Intestinal malrotation is treated surgically using the Ladd procedure. This procedure widens a fold in the peritoneum so that the intestines can be placed in non-rotated formation. Unfortunately, it is not possible to return the bowel to a normal morphology However, 89% of patients that undergo the Ladd surgery experience a complete resolution of symptoms.

Following cholangiogram, a Kasai Procedure is usually performed in cases of biliary atresia. In this surgery, a Y-shaped shunt is used to passage bile from the liver directly to the intestine. If this is unsuccessful, liver transplantation can be considered based on the overall health of the patient. Fortunately, the Kasai Procedure is successful in approximately 80% of patients. Following the operation, patients are advised to take fat-soluble vitamins, choleretics, and anti-inflammatory medications.

Functionally asplenic patients have an elevated lifetime risk of septicemia, as they have no functional spleen for fighting infection. For this reason, asplenic patients are under constant observation for any signs of fever or infection. In the case of infection, patients are placed on controlled empiric antibiotic therapy to avoid development of antibiotic resistance. This therapy battles infection by both gram-positive and gram-negative bacteria.

Right-atrial and left-atrial isomerism and associated pulmonary issues are treated in a series of steps based on the severity of symptoms. Isomeric patients are first treated by inserting a shunt that will move incoming blood through the pulmonary circuit. The Fontan procedure routes blood through the patient's single ventricle, to the lungs, and into systemic circulation. This process is favorable in patients aged 2 – 5 years old. Unfortunately, 20-30% of patients will require a heart transplant. Left-atrial isomeric patients have less severe complications, as they typically have 2 functional ventricles. In this case, they can undergo biventricular repair to form 2 separate ventricles and functional associated valves.

Prognosis for patients with situs ambiguous is quite varied, considering the spectrum of clinical complications. Infants who experience severe cyanosis at birth die within hours of delivery if medical intervention is not immediate. Alternatively, longevity of neonates with mild cardiac lesions is unaffected. Ten percent of patients born with right atrial isomerism die by the age of 5 without intervention. Fortunately, improvements in therapies has increased the 5-year survival to 30-74% for right atrial isomeric patients and 65-84% for left atrial isomeric patients based on the cause of their disease.

Pharmacologic management of ARVD involves arrhythmia suppression and prevention of thrombus formation.

Sotalol, a beta blocker and a class III antiarrhythmic agent, is the most effective antiarrhythmic agent in ARVD. Other antiarrhythmic agents used include amiodarone and conventional beta blockers (i.e.: metoprolol). If antiarrhythmic agents are used, their efficacy should be guided by series ambulatory holter monitoring, to show a reduction in arrhythmic events.

While angiotensin converting enzyme inhibitors (ACE Inhibitors) are well known for slowing progression in other cardiomyopathies, they have not been proven to be helpful in ARVD.

Individuals with decreased RV ejection fraction with dyskinetic portions of the right ventricle may benefit from long term anticoagulation with warfarin to prevent thrombus formation and subsequent pulmonary embolism.

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 primary goal of medications is to relieve symptoms such as chest pain, shortness of breath, and palpitations. Beta blockers are considered first-line agents, as they can slow down the heart rate and decrease the likelihood of ectopic beats. For people who cannot tolerate beta blockers, nondihydropyridine calcium channel blockers such as verapamil can be used, but are potentially harmful in people who also have low blood pressure or severe shortness of breath at rest. These medications also decrease the heart rate, though their use in people with severe outflow obstruction, elevated pulmonary artery wedge pressure, and low blood pressures should be done with caution. Dihydropyridine calcium channel blockers should be avoided in people with evidence of obstruction. For people whose symptoms are not relieved by the above treatments, disopyramide can be considered for further symptom relief. Diuretics can be considered for people with evidence of fluid overload, though cautiously used in those with evidence of obstruction. People who continue to have symptoms despite drug therapy can consider more invasive therapies. Intravenous phenylephrine (or another pure vasoconstricting agent) can be used in the acute setting of low blood pressure in those with obstructive hypertrophic cardiomyopathy who do not respond to fluid administration.

Catheter ablation may be used to treat intractable ventricular tachycardia.

It has a 60–90% success rate. Unfortunately, due to the progressive nature of the disease, recurrence is common (60% recurrence rate), with the creation of new arrhythmogenic foci. Indications for catheter ablation include drug-refractory VT and frequent recurrence of VT after ICD placement, causing frequent discharges of the ICD.

Head circumference measurements should be obtained regularly and monitored carefully to detect hydrocephalus. Neurosurgical procedures to relieve hydrocephalus are important. A ventriculoperitoneal shunt may be required in some infants. A pediatric cardiologist should be consulted to manage high-output failure, if present. Often patients need to be intubated. In most cases, the fistulous arteries feeding into the Vein of Galen must be blocked, thereby reducing the blood flow into the vein. Open surgery has a high morbidity and mortality. Recent advances over the past few decades have made endovascular embolization the preferred method of treatment. These treatments are preferred because they offer little threat to the surrounding brain tissue. However, there have been several reported cases of arteriovenous malformations recurring. The young age of many patients, the complex vascular anatomy, and the sensitive location of the Vein of Galen offer considerable challenges to surgeons. Another treatment option is Radiotherapy. Radiotherapy, also called radiosurgery, involves the use of focused beams to damage the blood vessel. Radiotherapy is often not pursued as a treatment because the effects of the procedure can take months or years and there is risk of damaging adjacent brain tissue.

Surgery is not always an option when the anatomy of the malformation creates too much of a risk. Recent improvements in endovascular procedures have made many cases, which were not surgically accessible, treatable. Endovascular treatments involve delivering drugs, balloons, or coils to the site of the malformation through blood vessels via catheters. These treatments work by limiting blood flow through the vein. There is, however, still risk of complications from endovascular treatments. The wall of the vein can be damaged during the procedure and, in some cases, the emboli can become dislodged and travel through the vascular system. Two-dimensional echocardiography with color-flow imaging and pulsed Doppler ultrasound was used to evaluate one fetus and five neonates with a Vein of Galen malformation. Color-flow imaging and pulsed Doppler ultrasonography provided anatomical and pathophysiological information regarding cardiac hemodynamics and intracranial blood flow; with the patient's clinical status, these methods provided a reliable, noninvasive means to evaluate the effectiveness of therapy and the need for further treatment in neonates with Vein of Galen malformations. When none of these procedures are viable, shunting can be used to ameliorate the pressure inside the varix. Seizures usually are managed with antiepileptic medications.

Current treatment options for Boxer cardiomyopathy are largely restricted to the use of oral anti-arrhythmic medications. The aim of therapy is to minimize ventricular ectopy, eliminate syncopal episodes, and prevent sudden cardiac death. A number of medications have been used for this purpose, including atenolol, procainamide, sotalol, mexiletine, and amiodarone. Combinations can also be used. Sotalol is probably the most commonly used antiarrhythmic at this time. It has been demonstrated that sotalol alone, or a combination of mexiletine and atenolol, results in a reduction in the frequency and complexity of ventricular ectopy. It is likely that these medications also reduce syncopal episodes, and it is hoped this extends to a reduced risk of sudden death. Consequently, antiarrhythmic therapy is typically recommended by veterinary cardiologists for Boxer dogs with ARVC. Although relatively rare, oral antiarrhythmic medications may be proarrhythmic in some dogs; consequently, appropriate monitoring and follow-up is recommended.

The ideal therapy for Boxer cardiomyopathy would be implantation of an implantable cardioverter-defibrillator (ICD). This has been attempted in a limited number of dogs. Unfortunately, ICDs are programmed for humans and the algorithms used are not appropriate for dogs, increasing the risk of inappropriate shocks. In the future, reprogramming of ICDs may allow them to emerge as a viable option in the treatment for Boxer cardiomyopathy.

A significant number of people with hypertrophic cardiomyopathy do not have any symptoms and will have normal life expectancies, although they should avoid particularly strenuous activities or competitive athletics, and should be screened for risk factors for sudden cardiac death. In people with resting or inducible outflow obstructions, situations that will cause dehydration or vasodilation (such as the use of vasodilatory or diuretic blood pressure medications) should be avoided. Septal reduction therapy is not recommended in asymptomatic people.

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.

Treatment of restrictive cardiomyopathy should focus on management of causative conditions (for example, using corticosteroids if the cause is sarcoidosis), and slowing the progression of cardiomyopathy. Salt-restriction, diuretics, angiotensin-converting enzyme inhibitors, and anticoagulation may be indicated for managing restrictive cardiomyopathy.

Calcium channel blockers are generally contraindicated due to their negative inotropic effect, particularly in cardiomyopathy caused by amyloidosis. Digoxin, calcium channel blocking drugs and beta-adrenergic blocking agents provide little benefit, except in the subgroup of restrictive cardiomyopathy with atrial fibrillation. Vasodilators are also typically ineffective because systolic function is usually preserved in cases of RCM.

Heart failure resulting from restrictive cardiomyopathy will usually eventually have to be treated by cardiac transplantation or left ventricular assist device.

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.

As there is no known cure, Loeys–Dietz syndrome is a lifelong condition. Due to the high risk of death from aortic aneurysm rupture, patients should be followed closely to monitor aneurysm formation, which can then be corrected with interventional radiology or vascular surgery.

Previous research in laboratory mice has suggested that the angiotensin II receptor antagonist losartan, which appears to block TGF-beta activity, can slow or halt the formation of aortic aneurysms in Marfan syndrome. A large clinical trial sponsored by the National Institutes of Health is currently underway to explore the use of losartan to prevent aneurysms in Marfan syndrome patients. Both Marfan syndrome and Loeys–Dietz syndrome are associated with increased TGF-beta signaling in the vessel wall. Therefore, losartan also holds promise for the treatment of Loeys–Dietz syndrome. In those patients in which losartan is not halting the growth of the aorta, irbesartan has been shown to work and is currently also being studied and prescribed for some patients with this condition.

If an increased heart rate is present, atenolol is sometimes prescribed to reduce the heart rate to prevent any extra pressure on the tissue of the aorta. Likewise, strenuous physical activity is discouraged in patients, especially weight lifting and contact sports.

Treatment for brain AVMs can be symptomatic, and patients should be followed by a neurologist for any seizures, headaches, or focal neurologic deficits. AVM-specific treatment may also involve endovascular embolization, neurosurgery or radiosurgery.

Embolization, that is, cutting off the blood supply to the AVM with coils, particles, acrylates, or polymers introduced by a radiographically guided catheter, may be used in addition to neurosurgery or radiosurgery, but is rarely successful in isolation except in smaller AVMs. Gamma knife may also be used.

While Larsen syndrome can be lethal if untreated, the prognosis is relatively good if individuals are treated with orthopedic surgery, physical therapy, and other procedures used to treat the symptoms linked with Larsen syndrome.

Currently there is no cure for PWS. Treatment differs from person to person and depends on the extent and severity of the blood vessels malformations and the degree of correction possible. The treatments can only control for the symptoms and often involve a multidisciplinary care as mentioned in diagnosis. AVMs and AVFs are treated with surgery or with embolization. If there are differences in the legs because of overgrowth in the affected limb, then the patient is referred to an orthopedist. If legs are affected to a minimal degree, then the patient may find heel inserts to be useful as they adjust for the different lengths in the legs and can walk normally.The port-wine stains may be treated by dermatologists. Supportive care is necessary and may include compression garments. These garments are tight-fitting clothing on the affected limb and helps with reducing pain and swelling. This can also help with protecting the limb from bumps and scrapes that cause bleeding. Also again based on the symptoms, the doctors may recommend antibiotics or pain medications.

Surgical care might also be an option for PWS patients. Surgeons may perform debulking procedure in which abnormal and overgrown tissues are removed. If PWS is affecting a foot or leg, the limbs can become quite large. And orthopedic surgeon can operate on the limb to reshape the limb. If the growth of the limb is more than one inch a procedure called epiphysiodesis may be performed. This procedure interrupts the growth of the leg and stops the leg from growing too big.

Other treatment options include: embolization and laser therapy. Embolization includes a substance injected by an interventional radiologists that can help in the elimination of the abnormal connections between the arteries and veins. According to Parkes Weber syndrome—Diagnostic and management paradigms: A systematic review, published in July 2017, reported that embolization alone or in combination with surgical removal of arteriovenous malformations leads to significant clinical improvement. Laser therapy can also help lighten capillary malformations and can speed up the healing process of the bleeding lesions.

Also other specialists are needed for dealing with the progression of the disease such as: physical therapists, occupational therapists and counselors. Physical therapists can help ease the pain and increase the range of movements of the arm or leg that is overgrown. Occupational therapists could help with the development of motor skills impeded by physical problems. The classic port-wine stains may make the patient feel uncomfortable and counselors can help with the psychological and social issues.

PWS is a progressive condition and advances with age. It is dependent on: the extent of the disease and overgrowth, condition of the patient’s heart, if the blood vessels are responsive to treatment, overall health of the patient, tolerance of medications and treatments. Based on these factors the prognosis is fair to good. The deformity and overgrowth tend to progress with time until epiphyseal closure. A lot of medical attention is needed to correct the blood vessels.

Treatment for Larsen syndrome varies according to the symptoms of the individual. Orthopedic surgery can be performed to correct the serious joint defects associated with Larsen syndrome. Reconstructive surgery can be used to treat the facial abnormalities. Cervical kyphosis can be very dangerous to an individual because it can cause the vertebrae to disturb the spinal cord. Posterior cervical arthrodesis has been performed on patients with cervical kyphosis, and the results have been successful Propranolol has been used to treat some of the cardiac defects associated with Marfan's syndrome, so the drug also has been suggested to treat cardiac defects associated with Larsen syndrome.

Drug therapy can slow down progression and in some cases even improve the heart condition. Standard therapy may include salt restriction, ACE inhibitors, diuretics, and beta blockers. Anticoagulants may also be used for antithrombotic therapy. There is some evidence for the benefits of coenzyme Q10 in treating heart failure.

Sclerotherapy is a treatment for specific veins and vascular malformations in the affected area. It involves the injection of a chemical into the abnormal veins to cause thickening and obstruction of the targeted vessels. Such treatment may allow normal blood flow to resume. It is a non-surgical medical procedure and is not nearly as invasive as debulking. Ultrasound guided foam sclerotherapy is the state of the art new treatment which could potentially close many large vascular malformations.

Compression therapies are finding more use as of the last ten years. The greatest issue with KTS syndrome is that the blood flow and/or lymph flow may be impeded, and will pool in the affected area. This can cause pain, swelling, inflammations, and in some cases, even ulceration and infection. Among older children and adults, compression garments can be used to alleviate almost all of these, and when combined with elevation of the affected area and proper management, can result in a comfortable lifestyle for the patient without any surgery. Compression garments are also used lately after a debulking procedure to maintain the results of the procedure. For early treatment of infants and toddlers with KTS, custom compression garments are impractical because of the rate of growth. When children may benefit from compression therapies, wraps and lymphatic massage may be used. While compression garments or therapy are not appropriate for everyone, they are relatively cheap (compared to surgery), and have few side-effects. Possible side-effects include a slight risk that the fluids may simply be displaced to an undesirable location (e.g., the groin), or that the compression therapy itself further impedes circulation to the affected extremities.

Artificial pacemakers may be used in patients with intraventricular conduction delay, and implantable cardioverter-defibrillators in those at risk of arrhythmia. These forms of treatment have been shown to prevent sudden cardiac death, improve symptoms, and reduce hospitalization in patients with systolic heart failure.

Debulking has been the most common treatment for KTS for several decades and while improvements have been made, the procedure is still considered invasive and has several risks associated with it. More effective and less invasive treatment choices now exist for KTS patients and therefore debulking is generally only recommended as a last resort. Debulking operations can result in major deformities and also leave patients with permanent nerve damage.

Mayo Clinic has reported the largest experience in managing KTS with major surgery. In 39 years at Mayo clinic the surgery team evaluated 252 consecutive cases of KTS, of which only 145 (57.5%) could be treated by primary surgery. The immediate success rate for treating varicose veins was only 40%, excision of vascular malformation was possible in 60%, debulking operations in 65%, and correction of bone deformity and limb length correction (epiphysiodesis) had 90% success. All the procedures demonstrated high recurrence rate in the follow-up. Mayo clinic studies demonstrate that primary surgical management of KTS has limitations and non-surgical approaches need to be developed in order to offer a better quality of life for these patients. Major surgery including amputation and debulking surgery does not seem to offer any benefit on a long-term basis.

Many factors influence the time course and extent of remodeling, including the severity of the injury, secondary events (recurrent ischemia or infarction), neurohormonal activation, genetic factors and gene expression, and treatment. Medications may attenuate remodeling. Angiotensin-converting enzyme (ACE) inhibitors have been consistently shown to decrease remodeling in animal models or transmural infarction and chronic pressure overload. Clinical trials have shown that ACE inhibitor therapy after myocardial infarction leads to improved myocardial performance, improved ejection fraction, and decreased mortality compared to patients treated with placebo. Likewise, inhibition of aldosterone, either directly or indirectly, leads to improvement in remodeling. Carvedilol, a 3rd generation beta blocker, may actually reverse the remodeling process by reducing left ventricular volumes and improving systolic function. Early correction of congenital heart defects, if appropriate, may prevent remodeling, as will treatment of chronic hypertension or valvular heart disease. Often, reverse remodeling, or improvement in left ventricular function, will also be seen.

Management has three components: interventions before delivery, timing and place of delivery, and therapy after delivery.

In some cases, fetal therapy is available for the underlying condition; this may help to limit the severity of pulmonary hypoplasia. In exceptional cases, fetal therapy may include fetal surgery.

A 1992 case report of a baby with a sacrococcygeal teratoma (SCT) reported that the SCT had obstructed the outlet of the urinary bladder causing the bladder to rupture in utero and fill the baby's abdomen with urine (a form of ascites). The outcome was good. The baby had normal kidneys and lungs, leading the authors to conclude that obstruction occurred late in the pregnancy and to suggest that the rupture may have protected the baby from the usual complications of such an obstruction. Subsequent to this report, use of a vesicoamniotic shunting procedure (VASP) has been attempted, with limited success.

Often, a baby with a high risk of pulmonary hypoplasia will have a planned delivery in a specialty hospital such as (in the United States) a tertiary referral hospital with a level 3 neonatal intensive-care unit. The baby may require immediate advanced resuscitation and therapy.

Early delivery may be required in order to rescue the fetus from an underlying condition that is causing pulmonary hypoplasia. However, pulmonary hypoplasia increases the risks associated with preterm birth, because once delivered the baby requires adequate lung capacity to sustain life. The decision whether to deliver early includes a careful assessment of the extent to which delaying delivery may increase or decrease the pulmonary hypoplasia. It is a choice between expectant management and active management. An example is congenital cystic adenomatoid malformation with hydrops; impending heart failure may require a preterm delivery. Severe oligohydramnios of early onset and long duration, as can occur with early preterm rupture of membranes, can cause increasingly severe PH; if delivery is postponed by many weeks, PH can become so severe that it results in neonatal death.

After delivery, most affected babies will require supplemental oxygen. Some severely affected babies may be saved with extracorporeal membrane oxygenation (ECMO). Not all specialty hospitals have ECMO, and ECMO is considered the therapy of last resort for pulmonary insufficiency. An alternative to ECMO is high-frequency oscillatory ventilation.

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.