The syndrome has five characteristic findings:

- Omphalocele

- Anterior diaphragmatic hernia

- Sternal cleft with or without ectopia cordis

- Diaphragmatic pericardium defects (no diaphragmatic pericardium)

- Intracardiac defect: ventricular septal defect, diverticulum of the left ventricle, Tetralogy of Fallot

Intestinal atresias are often discovered before birth: either during a routine sonogram which shows a dilated intestinal segment due to the blockage, or by the development of polyhydramnios (the buildup of too much amniotic fluid in the uterus). These abnormalities are indications that the fetus may have a bowel obstruction which a more detailed ultrasound study can confirm.

Some fetuses with bowel obstruction have abnormal chromosomes. An amniocentesis is recommended because it can determine not only the sex of the baby, but whether or not there is a problem with the chromosomes.

Other birth defects may co-exist, particularly in the heart, but sometimes also in the anus, spinal column, or kidneys. This is known as VACTERL association because of the involvement of Vertebral column, Anorectal, Cardiac, Tracheal, Esophageal, Renal, and Limbs. It is associated with polyhydramnios in the third trimester.

The prognosis of ectopia cordis depends on classification according to three factors:

1. Location of the defect

- Cervical

- Thoracic

- Thoracoabdominal

- Abdominal

2. Extent of the cardiac displacement

3. Presence or absence of intracardiac defects

Some studies have suggested a better prognosis with surgery in cases of thoracoabdominal ectopia cordis or less severe pentalogy of Cantrell. In general, the prognosis for ectopia cordis is poor—most cases result in death shortly after birth due to infection, hypoxemia, or cardiac failure.

Any attempt at feeding could cause aspiration pneumonia as the milk collects in the blind pouch and overflows into the trachea and lungs. Furthermore, a fistula between the lower esophagus and trachea may allow stomach acid to flow into the lungs and cause damage. Because of these dangers, the condition must be treated as soon as possible after birth.

Due to the rarity and rapid postpartum mortality of ectopia cordis, limited treatment options have been developed. Only one successful surgery has been performed as of now, and the mortality rate remains high.

Surgical repair can sometimes result in complications, including:

- Stricture, due to gastric acid erosion of the shortened esophagus

- Leak of contents at the point of anastomosis

- Recurrence of fistula

- Gastro-esophageal reflux disease

- Dysphagia

- Asthma-like symptoms, such as persistent coughing/wheezing

- Recurrent chest infections

- Tracheomalacia

Atresia is a condition in which an orifice or passage in the body is (usually abnormally) closed or absent.

Examples of atresia include:

- Biliary atresia, a condition in newborns in which the common bile duct between the liver and the small intestine is blocked or absent.

- Choanal atresia, blockage of the back of the nasal passage, usually by abnormal bony or soft tissue.

- Esophageal atresia, which affects the alimentary tract and causes the esophagus to end before connecting normally to the stomach.

- Imperforate anus, malformation of the opening between the rectum and anus.

- Intestinal atresia, malformation of the intestine, usually resulting from a vascular accident in utero.

- Microtia, absence of the ear canal or failure of the canal to be tubular or fully formed (can be related to Microtia, a congenital deformity of the pinna, or outer ear).

- Ovarian follicle atresia, the degeneration and subsequent resorption of one or more immature ovarian follicles.

- Potter sequence, congenital decreased size of the kidney leading to absolutely no functionality of the kidney, usually related to a single kidney.

- Pulmonary atresia, malformation of the pulmonary valve in which the valve orifice fails to develop.

- Renal agenesis, only having one kidney.

- Tricuspid atresia, a form of congenital heart disease whereby there is a complete absence of the tricuspid valve, and consequently an absence of the right atrioventricular connection.

- Vaginal atresia, a congenital occlusion of the vagina or subsequent adhesion of the walls of the vagina, resulting in its occlusion.

The most common cause of non-duodenal intestinal atresia is a vascular accident in utero that leads to decreased intestinal perfusion and ischemia of the respective segment of bowel. This leads to narrowing, or in the most severe cases, complete obliteration of the intestinal lumen.

In the case that the superior mesenteric artery, or another major intestinal artery, is occluded, large segments of bowel can be entirely underdeveloped. Classically, the affected area of bowel assumes a spiral configuration and is described to have an "apple peel" like appearance; this is accompanied by lack of a dorsal mesentery.

Ileal atresia can also result as a complication of meconium ileus.

Fistulae between the trachea and esophagus in the newborn can be of diverse morphology and anatomical location; however, various pediatric surgical publications have attempted a classification system based on the below specified types.

Not all types include both esophageal agenesis and tracheoesophageal fistula, but the most common types do.

The letter codes are usually associated with the system used by Gross, while number codes are usually associated with Vogt.

An additional type, "blind upper segment only" has been described, but this type is not usually included in most classifications.

A left ventricular outflow tract obstruction (LVOTO) may be due to a defect in the aortic valve, or a defect located at the subvalvar or supravalvar level.

- Aortic valve stenosis

- Supravalvar aortic stenosis

- Coarctation of the aorta

- Hypoplastic left heart syndrome

A right ventricular outflow tract obstruction (RVOTO) may be due to a defect in the pulmonic valve, the supravalvar region, the infundibulum, or the pulmonary artery.

- Pulmonary atresia

- Pulmonary valve stenosis

- Hypoplastic right heart syndrome

- Tetralogy of Fallot

Symptoms include difficulty breathing (dyspnea) and bluish discoloration on skin and lips (cyanosis). A newborn baby will show signs of heart failure such as edema, fatigue, wheezing, sweating and irregular heartbeat.

Anal atresia or imperforate anus is seen in about 55 percent of patients with VACTERL association. These anomalies are usually noted at birth and often require surgery in the first days of life. Sometimes babies will require several surgeries to fully reconstruct the intestine and anal canal.

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.

A diagnosis of pentalogy of Cantrell can often be made before birth (prenatally) sometimes using a fetal ultrasound. An ultrasound is an exam that uses high-frequency sound waves to produce an image of the developing fetus. A fetal ultrasound can detect some of the defects associated with pentalogy of Cantrell. An echocardiography is usually performed to evaluate the extent of the involvement of the heart. An echocardiography is an exam that uses sound waves to produce images of the heart

Magnetic resonance imaging (MRI) may also be performed to assess the degree of certain anomalies such as abdominal wall and pericardial defects. An MRI uses a magnetic field and radio waves to produce cross-sectional images of particular organs and bodily tissues.

The diagnosis of duodenal atresia is usually confirmed by radiography. An X-ray of the abdomen shows two large air filled spaces, the so-called "double bubble" sign. The air is trapped in the stomach and proximal duodenum, which are separated by the pyloric sphincter, creating the appearance of two bubbles visible on x-ray. Since the closure of the duodenum is complete in duodenal atresia, no air is seen in the distal duodenum.

Atresias occurring distal to the duodenum are usually caused by vascular accidents or ischemic insult, such as jejunoileal atresia.

Abdominal organs, including the liver, stomach, intestinal tract, and spleen may be randomly arranged throughout the left-right axis of the body. Distribution of these organs largely dictates treatment, clinical outcomes, and further evaluation.

The liver is typically symmetrical across the left-right axis in patients with situs ambiguous, which is abnormal. A majority of left atrial isomeric patients have defects throughout the biliary tree, which is responsible for bile production, even when the gall bladder is functional and morphologically normal. This biliary atresia can lead to acute problems such as nutrient malabsorption, pale stools, dark urine, and abdominal swelling. If this condition continues without proper treatment, cirrhosis and liver failure become a major concern. Biliary atresia is not usually observed in patients with right atrial isomerism.

Random positioning of the stomach is often one of the first signals of situs ambiguous upon examination. Malrotation of the entire intestinal tract, or improper folding and bulging of the stomach and intestines, results in bowel obstruction. This impairment leads to vomiting, abdominal distention, mucus and blood in the stool. Patients may also experience abdominal pain. Intestinal malrotation is more commonly identified in patients with right atrial isomerism than in those with left atrial isomerism.

Isomeric patients often experience disruptions to splenic development during embryogenesis, resulting in an overall lack a spleen (asplenia) or development of many spleens (polysplenia). Asplenia is most often observed in patients with right atrial isomerism. Polysplenia results in 90% of patients with left atrial isomerism. Although they have many spleens, each is usually ineffective resulting in functional asplenia. Rarely, left atrial isomeric patients have a single, normal, functional spleen. Patients lacking a functional spleen are in danger of sepsis and must be monitored.

During pregnancy, duodenal atresia is associated with increased amniotic fluid in the uterus, which is called polyhydramnios. This increase in amniotic fluid is caused by the inability of the fetus to swallow the amniotic fluid and absorb it in their digestive tract.

After birth, duodenal atresia may cause abdominal distension, especially of the upper abdomen. Bilious vomiting commonly occurs within the first day of life. The vomiting is described as "bilious", because it contains bile acid.

Vertebral anomalies, or defects of the spinal column, usually consist of small (hypoplastic) vertebrae or hemivertebra where only one half of the bone is formed. About 80 percent of patients with VACTERL association will have vertebral anomalies. In early life these rarely cause any difficulties, although the presence of these defects on a chest x-ray may alert the physician to other defects associated with VACTERL. Later in life these spinal column abnormalities may put the child at risk for developing scoliosis, or curvature of the spine.

If there is a defect in the septum, it is possible for blood to travel from the left side of the heart to the right side of the heart, or the other way around. Since the right side of the heart contains venous blood with a low oxygen content, and the left side of the heart contains arterial blood with a high oxygen content, it is beneficial to prevent any communication between the two sides of the heart and prevent the blood from the two sides of the heart from mixing with each other.

Symptoms are caused by vascular compression of the airway, esophagus or both. Presentation is often within the first month (neonatal period) and usually within the first 6 months of life. Starting at birth an inspiratory and expiratory stridor (high pitch noise from turbulent airflow in trachea) may be present often in combination with an expiratory wheeze. The severity of the stridor may depend on the patient’s body position. It can be worse when the baby is lying on his back rather than its side. Sometimes the stridor can be relieved by extending the neck (lifting the chin up). Parents may notice that the baby’s cry is hoarse and the breathing noisy. Frequently a persistent cough is present. When the airway obstruction is significant there may be episodes of severe cyanosis (“blue baby”) that can lead to unconsciousness. Recurrent respiratory infections are common and secondary pulmonary secretions can further increase the airway obstruction.

Secondary to compression of the esophagus babies often feed poorly. They may have difficulties in swallowing liquids with choking or regurgitating and increased respiratory obstruction during feeding. Older patients might refuse to take solid food, although most infants with severe symptoms nowadays are operated upon before they are offered solid food.

Occasionally patients with double aortic arches present late (during later childhood or adulthood). Symptoms may mimic asthma.

Tetralogy of Fallot results in low oxygenation of blood due to the mixing of oxygenated and deoxygenated blood in the left ventricle via the ventricular septal defect (VSD) and preferential flow of the mixed blood from both ventricles through the aorta because of the obstruction to flow through the pulmonary valve. This is known as a right-to-left shunt. The primary symptom is low blood oxygen saturation with or without cyanosis from birth or developing in the first year of life. If the baby is not cyanotic then it is sometimes referred to as a "pink tet". Other symptoms include a heart murmur which may range from almost imperceptible to very loud, difficulty in feeding, failure to gain weight, retarded growth and physical development, dyspnea on exertion, clubbing of the fingers and toes, and polycythemia. The baby may turn blue with breast feeding or crying.

Children with tetralogy of Fallot may develop "tet spells". These are acute hypoxia spells, characterized by shortness of breath, cyanosis, agitation, and loss of consciousness. This may be initiated by any event leading to decreased oxygen saturation or that causes decreased systemic vascular resistance, leading to increased venous return, which in turn leads to increased shunting through the ventricular septal defect.

Tet spells are characterized by a sudden, marked increase in cyanosis followed by syncope, and may result in hypoxic brain injury and death.

Older children will often squat during a tet spell. This increases systemic vascular resistance and allows for a temporary reversal of the shunt. It increases pressure on the left side of the heart, decreasing the right to left shunt thus decreasing the amount of deoxygenated blood entering the systemic circulation.

CXR : decreased pulmonary blood flow and oligemic lung field

ECG : left axis deviation