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.

Sept. 29, 2026
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