There are a variety of clinical manifestations of situs ambiguous. Acute symptoms can be due to both cardiac and non-cardiac defects. Cyanosis or blue skin coloration, primarily affecting the lips and fingernails, can indicate a systemic or circulatory issue. Poor feeding, failure to thrive, and rapid shallow breathing may also be observed due to poor circulation. Upon examination, arrhythmia and heart murmur may raise further suspicion of a cardiac abnormality. Non-cardiac symptoms include impairments of the liver and gastrointestinal tract. Biliary atresia, or inflammation and destruction of the bile ducts, may lead to jaundice. Vomiting and swelling of the abdominal region are features that suggest improper positioning of the intestines. Poor positioning of the intestine also makes it more prone to blockage, which can result in numerous chronic health issues. Asplenia and polysplenia are also possible features of heterotaxy syndrome.

Due to abnormal cardiac development, patients with situs ambiguous usually develop right atrial isomerism consisting of 2 bilaterally paired right atria, or left atrial isomerism consisting of 2 bilaterally paired left atria. Clinical features and symptoms can vary dependent upon assignment of left versus right atrial isomerism. In either instance, the apex of the heart will be poorly positioned, which should alert a clinician of the likelihood of atrial isomerism. It is estimated that 5-10% of isomeric patients have mesocardia, in which the heart is positioned at the center of the thorax, 25-50% have dextrocardia, in which the apex of the heart is pointed toward the right side of the thorax, and 50 - 70% have levocardia, in which the apex of the heart is pointed toward the left side of the thorax.

Situs ambiguus or situs ambiguous, also known as heterotaxy or heterotaxia, is a rare congenital defect in which the major visceral organs are distributed abnormally within the chest and abdomen. Heterotaxy in general refers to any defect of left-right laterality and arrangement of the visceral organs. This does not include the congenital defect situs inversus, which results when arrangement of the organs in the abdomen and chest are mirrored, so the positions are opposite the normal placement. Situs inversus is the mirror image of situs solitus, which is normal asymmetric distribution of the abdominothoracic visceral organs. Patients with situs ambiguous are considered isomeric in that they have organs with two right-sides or two left-sides, most commonly observed in relation to the atria of the heart.

Individuals with situs inversus or situs solitus do not experience fatal dysfunction of their organ systems, as general anatomy and morphology of the abdominothoracic organ-vessel systems are conserved. Due to abnormal arrangement of organs in situs ambiguous, orientation across the left-right axis of the body is disrupted early in fetal development, resulting in severely flawed cardiac development and function in 50–80% of cases. They also experience complications with systemic and pulmonary blood vessels, significant morbidity, and sometimes death. All patients with situs ambiguus lack lateralization and symmetry of organs in the abdominal and thoracic cavities and are clinically considered to have a form of heterotaxy syndrome.

Heterotaxy syndrome with atrial isomerism occurs in 1 out of every 10,000 live births and is associated with approximately 3% of congenital heart disease cases. Additional estimation of incidence and prevalence of isomerism proves difficult due to failure to diagnose and underestimation of the disease by clinicians. Furthermore, right isomerism is much more easily recognized than left isomerism, contributing to the failure to diagnose.

Situs ambiguous is a growing field of research with findings dating back to 1973.

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.

The condition affects all major structures within the thorax and abdomen. Generally, the organs are simply transposed through the sagittal plane. The heart is located on the right side of the thorax, the stomach and spleen on the right side of the abdomen and the liver and gall bladder on the left side. The heart's normal right atrium occurs on the left, and the left atrium is on the right. The lung anatomy is reversed and the left lung has three lobes while the right lung has two lobes. The intestines and other internal structures are also reversed from the normal, and the blood vessels, nerves, and lymphatics are also transposed.

If the heart is swapped to the right side of the thorax, it is known as "situs inversus with dextrocardia" or "situs inversus totalis". If the heart remains on the normal left side of the thorax, a much more rare condition (1 in 2,000,000 of the general population), it is known as "situs inversus with levocardia" or "situs inversus incompletus".

Situs inversus of the optic disc may occur unilaterally or bilaterally, associated with reduced binocularity and stereoacuity resembling monofixation syndrome. It is characterized by emergence of the retinal vessels in an anomalous direction (from the nasal rather than the temporal aspect) with dysversion (tilt) of the optic disc.

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.