Heterotaxy syndrome

Heterotaxy syndrome affects how organs form and where they are located in the body. Learn about symptoms, causes, diagnosis, treatment and care.

Update Date: 29.09.2026

Overview
Symptoms
Causes
Risk factors
Complications
Prevention
Diagnosis
Treatment
Lifestyle and home remedies
Coping and support
Preparing for an appointment

Overview

Heterotaxy syndrome is a rare condition that develops in an unborn baby, called a fetus, before birth. It affects how some organs form and where they are located in the body. Heterotaxy also is called situs ambiguus.

Heterotaxy can affect the heart, major blood vessels, spleen, liver, intestines and lungs. Heart conditions are common and often have the greatest effect on a person's health. Some people with heterotaxy have mild health conditions. Others have serious heart or other organ conditions that need ongoing care.

Heterotaxy is different for each person. Because it can affect several parts of the body in different ways, the care team looks closely at each organ and builds a treatment plan around that person's needs.

Some parts of the body usually have different features on the right and left sides. For example, small structures attached to the heart's upper chambers have a different shape on each side. With heterotaxy, the structures on both sides may have features that usually occur on the right or features that usually occur on the left. This pattern is called isomerism.

Heterotaxy is rare. It occurs in about 1 in 10,000 babies born.

Types

Heterotaxy is often grouped into two types. These types are based on small structures attached to the heart's two upper chambers, called atria. These structures usually have a different shape on the right and left sides of the heart. In heterotaxy, the structures on both sides may include features usually found on the right or features usually found on the left.

Right atrial isomerism (RAI)

In RAI, the structures attached to both atria have features usually found on the right side. Heart conditions are often complex. For example, only one lower heart chamber may be able to pump well. Blood flow to the lungs may be limited. The blood vessels that carry blood from the lungs also may connect to the heart in an unusual way.

People with RAI also are often missing their spleen. This is called asplenia.

People with RAI also may have a condition that affects the center of the heart, called an atrioventricular canal defect.

Left atrial isomerism (LAI)

In LAI, the structures attached to both atria have features usually found on the left side. Heart structure varies widely. Some people have two lower heart chambers that can pump well. Others have differences in a large vein that carries blood back to the heart, called the inferior vena cava. A slow heartbeat or other changes in the heart's electrical system also may occur.

People with LAI often have several spleens. This is called polysplenia.

These types can help describe heterotaxy, but they do not predict every heart or organ issue. Each person can have a different mix of heart, spleen and other organ conditions. The care team checks each organ rather than relying on the type alone.

Symptoms

The signs and symptoms of heterotaxy depend on which organs are affected and how they affect a person's health. Some babies have few clear signs at birth. Others become ill soon after they are born.

Symptoms related to the heart may include:

  • Gray or blue skin, lip or nail bed color caused by low oxygen in the blood. This is called cyanosis.
  • Fast or difficult breathing.
  • A heartbeat that is too slow, too fast or not regular.
  • In older children or adults, a racing or pounding heartbeat, dizziness, fainting or shortness of breath.

Symptoms related to other organs may include:

  • Fever or a serious infection when the spleen is missing or does not work well. The spleen helps the body fight certain infections.
  • Pain in the abdomen. Some people with heterotaxy have intestines that did not form in their usual position. This is called intestinal malrotation. In some cases, the intestine can twist. This is called volvulus.
  • Green vomit or trouble feeding. These also can be signs that the intestines are blocked or twisted.
  • Yellowing of the skin or eyes, called jaundice. In a baby with heterotaxy, jaundice can be a sign of biliary atresia, a condition in which tubes that carry bile from the liver are blocked or missing.

When to seek care

Call your care team if you notice new or worsening symptoms, such as:

  • Trouble breathing.
  • Trouble feeding.
  • A racing or pounding heartbeat.
  • Dizziness.
  • Fainting.
  • Vomiting.
  • Yellowing of the skin or eyes, called jaundice.

If the spleen is missing or does not work well, get prompt medical care for a fever. Without a working spleen, an infection can become serious quickly.

When to seek emergency care

Seek emergency medical care for:

  • Severe trouble breathing.
  • A clear change in skin color to gray or blue.
  • Green vomit along with severe stomach symptoms. Green vomit can be a sign that the intestine is blocked or twisted.

Causes

Heterotaxy starts very early in pregnancy, as the baby's left and right sides begin to develop. Signals in the body help guide where organs form and how they develop. Changes in these signals can lead to heterotaxy. For many people, the exact cause is not known.

Genes can play a role. Some gene changes affect the signals that guide how the left and right sides of the body develop. Other gene changes affect cilia. Cilia are tiny, hairlike structures on cells that help guide how the left and right sides of the body develop.

Some forms of heterotaxy can be inherited, depending on the gene involved. But not everyone with heterotaxy inherited the condition from a parent.

A genetic counselor or other member of your care team can help you decide whether genetic testing may be useful. Your care team also can explain what test results may mean for the person with heterotaxy and for future pregnancies.

Risk factors

There are no known lifestyle factors that cause heterotaxy.

In some families, the chance of heterotaxy may be higher when there is a family history of:

  • Heterotaxy.
  • Heart conditions present at birth, called congenital heart disease.
  • Differences in how organs developed on the left and right sides of the body.

The chance of heterotaxy happening again in a family depends in part on whether a specific genetic cause is found. Genetic counseling can help families review their health history, consider genetic testing and learn more about the chance of heterotaxy in a future pregnancy.

Complications

Heterotaxy can affect several parts of the body. The possible complications depend on which organs are affected. They may include:

  • Complex heart conditions, low blood oxygen or heart failure.
  • A heartbeat that is too fast, too slow or not regular.
  • A serious change in the heart's electrical signals called complete heart block. In this condition, the electrical signals that control the heartbeat are blocked.
  • Blood vessels that are blocked or connected in an unusual way. For example, the veins that carry blood from the lungs to the heart may not connect as expected.
  • A higher risk of serious infections if the spleen is missing or does not work well. A serious infection can sometimes lead to sepsis, a life-threatening reaction to infection.
  • A blocked or twisted intestine related to intestines that did not form in their usual position.
  • Biliary atresia, which can lead to liver disease.
  • Heart conditions that develop or continue after surgery, such as a leaky heart valve, changes in heart rhythm or heart failure.

Prevention

There is no known way to prevent heterotaxy syndrome.

If a family has a child with heterotaxy or a known gene change linked to the condition, genetic counseling before or during a future pregnancy can help. A genetic counselor can explain testing options and the chance of heterotaxy happening again in the family.

Diagnosis

Heterotaxy may be found before birth or after birth. Because it can affect each person differently, the care team needs a clear picture of the heart, blood vessels and other organs. Tests help the team understand which parts of the body are affected and plan the care each person needs.

Testing before birth

An ultrasound during pregnancy may show that the heart, stomach or other organs are in different positions than expected. If your care team suspects heterotaxy, more tests can help the team learn about the baby's heart and other organs.

A fetal echocardiogram is a detailed ultrasound of the baby's heart. It can show the heart, how blood flows through it and how major blood vessels connect to it. A fetal echocardiogram helps the care team understand the structure of the baby's heart and plan the right care.

In some cases, a fetal MRI can give the care team a closer look at the baby's organs. This information can help the team and family plan for the baby's care before and after birth.

Testing after birth

After birth, an echocardiogram is one of the main tests used to check the heart. It uses sound waves to show how the heart formed, how well it pumps, how blood flows through it and how the major blood vessels connect.

Other tests may include:

  • Pulse oximetry. This measures the amount of oxygen in the blood.
  • An electrocardiogram (ECG or EKG). This test checks the heart's electrical activity and rhythm.
  • A chest X-ray. This gives the care team a picture of the heart and lungs.

Some people may need a cardiac MRI or a CT scan. These tests can give the care team a closer look at the heart and blood vessels. Cardiac catheterization uses a thin, flexible tube called a catheter to examine the heart. This may be used when the care team needs more information about blood flow or pressure inside the heart and blood vessels.

Checking other organs

The care team also checks organs outside the heart. The team does not assume which organs are affected based only on the type of heterotaxy.

Imaging and blood tests can help the team find out whether a spleen is present and how well it works. Babies with jaundice may need tests for biliary atresia.

Green vomit, trouble feeding or other signs of an intestinal blockage may mean that the intestines need to be checked. Your care team may recommend a type of X-ray that can show whether the intestines are in an unusual position or have become twisted. This is called an upper gastrointestinal (GI) contrast study.

Genetic testing

Your care team may recommend genetic testing based on the specific health condition and your family history. Testing may help find a genetic cause for heterotaxy. It also can give you more information about whether the condition could occur again in a future pregnancy.

Treatment

Treatment for heterotaxy is different for each person. Your care team builds a plan based on how the heart formed, which other organs are affected and how well they work. Some people need little treatment, while others need medicines, procedures or surgery. Babies with complex heart conditions need care from a team experienced in congenital heart disease.

Medicines

Some newborns with heterotaxy have heart conditions that limit blood flow to the lungs. They may receive a medicine called prostaglandin E1, also known as alprostadil.

This medicine keeps a blood vessel called the ductus arteriosus open. Keeping this blood vessel open allows blood to continue reaching the lungs. The medicine typically is used until surgery or a heart catheter procedure can provide another path for blood to reach the lungs.

Other medicines and breathing support may be used to help the heart work and keep the baby stable.

People whose spleen is missing or does not work well may need antibiotics to help prevent serious infections. Certain vaccines also can help protect against infection.

Changes in heart rhythm may be treated with medicine or a pacemaker, depending on the type of rhythm change.

Heart procedures and surgery

Heart surgery is planned around the structure of each person's heart and blood vessels. The goal is to create the best possible path for blood to flow through the heart, lungs and body.

Two-ventricle repair. When both lower chambers of the heart, called ventricles, can pump well, surgeons may be able to use both chambers to support blood flow. This is called a two-ventricle repair or biventricular repair.

Single-ventricle palliation. When only one ventricle can do the work needed to pump blood, treatment may involve a series of surgeries called single-ventricle palliation. These surgeries change the path of blood flow so blood can reach the lungs.

The surgeries needed, and the timing of those surgeries, depend on the person's heart and blood vessels. They may include:

  • Bidirectional cavopulmonary connection. This procedure directs blood from the upper part of the body straight to the lungs.
  • Kawashima procedure. For some people with differences in the large veins that return blood to the heart, this procedure directs much of the returning blood straight to the lungs.
  • Fontan procedure. This procedure is usually a later stage of treatment. It directs most of the blood returning from the body straight to the lungs without first passing through a ventricle.

Some people may eventually need a heart transplant.

Some changes in heart rhythm can be treated with cardiac ablation. During this procedure, a doctor guides a thin tube called a catheter into the heart. The doctor then uses radiofrequency energy to treat a small area of heart tissue that is causing the rhythm change. Veins may connect differently or be blocked in people with heterotaxy. Because of this, the care team may need to use a different approach to guide the catheter to the heart.

Heart surgery for heterotaxy can be complex, and some people need more surgeries or catheter procedures over time. What to expect depends on the structure of the person's heart, other health conditions and how well treatment works. Your care team can explain what these factors may mean for you or your child.

Treatment of other organ conditions

If the spleen is missing or does not work well, a fever needs prompt medical care. Your care team can tell you what to do if a fever develops. Antibiotics may be needed to treat an infection.

If the intestine becomes twisted or blocked because of intestinal malrotation, surgery may be needed. One type of surgery, called a Ladd procedure, places the intestines in a safer position and treats the blockage or twisting.

If intestinal malrotation is not causing symptoms, surgery to prevent a future blockage or twisting may not be recommended. The care team considers each person's health and anatomy when deciding whether surgery is needed.

Biliary atresia needs prompt care from a specialist. If testing confirms the condition, surgery is needed.

Prognosis

The outlook for people with heterotaxy varies widely. Some people have mild health conditions. Others have complex heart conditions or other organ conditions that can be life-threatening. A person's life expectancy depends on which organs are affected, how the heart is structured, how well the organs work and how the person responds to treatment.

Survival rates can give a broad picture of outcomes for groups of people with heterotaxy, but they cannot predict what will happen to one person.

Treatment and care for heterotaxy continue to improve, and more people with the condition are living into adulthood. Still, heterotaxy can be a serious lifelong condition, especially when the heart is greatly affected.

Some severe heart conditions linked to heterotaxy need treatment early in life to provide enough blood flow and oxygen to the body. The care team can explain how a person's specific heart and organ findings may affect what to expect over time.

People with heterotaxy need lifelong follow-up care, even when treatment goes well. This may include checking heart function, heart valves and rhythm, oxygen levels, and other organs. Regular follow-up helps your care team watch for changes and decide whether more treatment is needed.

Lifestyle and home remedies

Living with heterotaxy often means keeping track of care from several specialists. Following the care plan and knowing what to watch for can help you or your child get the right care when it is needed.

Keep vaccines and medicines that help prevent infection up to date, especially if the spleen is missing or does not work well.

Keep an up-to-date summary of important health information, including:

  • The structure of the heart and blood vessels.
  • Surgeries and catheter procedures.
  • Medicines.
  • Instructions for urgent or emergency care.

Share this information with healthcare professionals who are new to your care team. It can help them understand your or your child's anatomy, health history and care needs.

Coping and support

You may find that talking with other people who've been in the same situation brings you comfort and encouragement. Ask your healthcare team if there are any support groups in your area. You also may be able to find online support groups.

Living with or caring for someone with heterotaxy can make some people feel stressed or anxious. Talking with a therapist or counselor may help you learn new ways to manage stress and anxiety. Ask your care team to recommend a therapist who may help you or your child.

Preparing for an appointment

Bringing key health information and a list of questions can help you make the most of appointments.

What you can do

Before an appointment:

  • Make a list of related health information. This may include health conditions, surgeries, catheter procedures, medicines and allergies.
  • Gather recent test results and procedure records if you have them. These may include ECG, surgery, catheterization and imaging test results.
  • Write down any new or worsening symptoms, including changes in breathing, feeding, growth, ability to exercise, heartbeat or skin color, as well as fever or vomiting.

Questions you may want to ask:

  • Has the spleen been checked, and how well does it work?
  • What should I do if a fever develops?
  • Are the intestines at risk of becoming blocked or twisted?
  • Which specialists should be involved?
  • How often is follow-up needed?
  • Would genetic counseling or testing be helpful?

What your healthcare professional may ask

Be ready to answer questions such as:

  • When was heterotaxy first suspected or diagnosed?
  • What have you been told about the heart and blood vessels?
  • Have you noticed a change in skin color, trouble breathing, fainting or changes in heartbeat?
  • Has there been fever, green vomit, trouble feeding or jaundice?
  • What surgeries, catheter procedures or other treatments have been done?
  • Is there a family history of heterotaxy, congenital heart disease or differences in how organs developed on the left and right sides of the body?

© 2026 Mayo Foundation for Medical Education and Research. All rights reserved. Terms of Use