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.

Situs inversus is generally an autosomal recessive genetic condition, although it can be X-linked or found in identical "mirror image" twins.

About 25% of individuals with situs inversus have an underlying condition known as primary ciliary dyskinesia (PCD). PCD is a dysfunction of the cilia that manifests itself during the embryologic phase of development. Normally functioning cilia determine the position of the internal organs during early embryological development, and so embryos with PCD have a 50% chance of developing situs inversus. If they do, they are said to have Kartagener syndrome, characterized by the triad of situs inversus, chronic sinusitis, and bronchiectasis. Cilia are also responsible for clearing mucus from the lung, and the dysfunction causes increased susceptibility to lung infections. Kartagener syndrome can also manifest with male infertility as functional cilia are required for proper sperm flagella function.

Several genes have been identified in normal development of the right-left axis. These genes have been extensively researched. Gene mutations that lead to atrial isomerism is a growing area of research. Mutations in genes that encode proteins in the TGF-beta pathway, including NODAL, NKX2-5, and ZIC3, have been linked to tetralogy of fallot and hypoplastic left heart syndrome. Mutations in the ZIC3 gene, which encodes for the first zinc finger transcription factor, is linked to a 50% risk of atrial isomerism in families. It is also an X-linked disorder, so testing for ZIC3 mutations is highly encouraged in male births.

The most prevalent and best characterized genetic associations of heterotaxy include:

Levocardia is a medical condition where the heart is on the normal side of the body (the left), as opposed to dextrocardia, in which the heart is in the right side of the thoracic cavity. This can be associated with "situs solitus", where the remainder of the organs are on normal side as well; or "situs inversus", in which the viscera (stomach, liver, intestines, lungs, etc.) on the opposite side as normal. The latter condition may or may not be associated with clinically relevant abnormalities.

In the absence of congenital heart defects, individuals with situs inversus are phenotypically normal, and can live normal healthy lives, without any complications related to their medical condition. There is a 5–10% prevalence of congenital heart disease in individuals with situs inversus totalis, most commonly transposition of the great vessels. The incidence of congenital heart disease is 95% in situs inversus with levocardia.

Many people with situs inversus totalis are unaware of their unusual anatomy until they seek medical attention for an unrelated condition, such as a rib fracture or a bout of appendicitis. The condition may also be discovered during the administration of certain medicines or during tests such as a Barium meal or enema. The reversal of the organs may then lead to some confusion, as many signs and symptoms will be on the atypical side. For example, if an individual with situs inversus develops appendicitis, they will present to the physician with lower left abdominal pain, since that is where their appendix lies. Thus, in the event of a medical problem, the knowledge that the individual has situs inversus can expedite diagnosis. People with this rare condition should inform their doctors before an examination, so the doctor can redirect their search for heart sounds and other signs. Wearing a medical identification tag can help inform health care providers in the event the person is unable to communicate.

Situs inversus also complicates organ transplantation operations as donor organs will more likely come from situs solitus (normal) donors. As hearts and livers are chiral, geometric problems arise placing an organ into a cavity shaped in the mirror image. For example, a person with situs inversus who requires a heart transplant needs all the vessels to the transplant donor heart reattached to their existing ones. However, the orientation of these vessels in a person with situs inversus is reversed, necessitating steps so that the blood vessels join properly.