Laryngeal cleft is usually diagnosed in an infant after they develop problems with feeding, such as coughing, cyanosis (blue lips) and failing to gain weight over time. Pulmonary infections are also common. The longer the cleft, the more severe are the symptoms. Laryngeal cleft is suspected after a video swallow study (VSS) shows material flowing into the airway rather than the esophagus, and diagnosis is confirmed through endoscopic examination, specifically microlaryngoscopy and bronchoscopy. If a laryngeal cleft is not seen on flexible nasopharyngoscopy, that does not mean that there is not one there. Laryngeal clefts are classified into four types according to Benjamin and Inglis. Type I clefts extend down to the vocal cords; Type II clefts extend below the vocal cords and into the cricoid cartilage; Type III clefts extend into the cervical trachea and Type IV clefts extend into the thoracic trachea. Subclassification of type IV clefts into Type IVA (extension to 5 mm below the innomate artery) and Type IV B (extension greater than 5 mm below the innominate artery) may help with preoperative selection of those who can be repaired via transtracheal approach (Type IV A) versus a cricotracheal separation approach (type IV B).

A laryngeal cleft or laryngotracheoesophageal cleft is a rare congenital abnormality in the posterior laryngo-tracheal wall. It occurs in approximately 1 in 10,000 to 20,000 births. It means there is a communication between the oesophagus and the trachea, which allows food or fluid to pass into the airway.

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.

This birth defect arises in the fourth fetal week, when the trachea and esophagus should begin to separate from each other.

It can be associated with disorders of the tracheoesophageal septum.

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.

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

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.

Tracheoesophageal fistula is suggested in a newborn by copious salivation associated with choking, coughing, vomiting, and cyanosis coincident with the onset of feeding. Esophageal atresia and the subsequent inability to swallow typically cause polyhydramnios in utero. Rarely it may present in an adult.

Tracheal agenesis is a rare birth defect with a prevalence of less than 1 in 50,000, in which the trachea fails to develop. The defect is normally fatal, although occasional cases have been reported of long-term survival following surgical intervention.

There are three main types of tracheal agenesis, designated Types I, II and III.

In 2013, a case was reported of a South Korean child with tracheal agenesis who had been successfully treated after having been kept alive in an intensive care unit for the first two and a half years of her life. She then had an artificially created trachea implanted that had been created by tissue engineering using her own stem cells. The patient however later died from complications.

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.

This condition exists in a variety of forms, ranging from partial absence of the tail bone regions of the spine to absence of the lower vertebrae, pelvis and parts of the thoracic and/or lumbar areas of the spine. In some cases where only a small part of the spine is absent, there may be no outward sign of the condition. In cases where more substantial areas of the spine are absent, there may be fused, webbed, or smaller lower extremities and paralysis. Bowel and bladder control is usually affected.

Infants with vascular rings typically present before 12 months with respiratory or esophageal symptoms like stridor, wheezing, cough, dysphagia, or difficulty feeding. The stridor improves with neck extension, differentiating from laryngomalacia which is relieved by prone or upright positioning, and will not be relieved with corticosteroids or epinephrine, unlike croup. Diagnosis requires a high degree of clinical suspicion and can be confirmed with barium contrast esophagogram for those with esophageal symptoms, bronchoscopy, or CT or MRI.

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.

Caudal regression syndrome or sacral agenesis (or hypoplasia of the sacrum) is a congenital disorder in which there is abnormal fetal development of the lower spine—the caudal partition of the spine.

It occurs at a rate of approximately one per 25,000 live births.

The two arches surround the esophagus and trachea which, if sufficiently constrictive, may cause breathing or swallowing difficulties despite medical therapies.

A less common ring is present with a right aortic arch instead of the usual left-sided aortic arch. This compresses the esophagus and trachea because of the persistence of a ductal ligament (from fetal circulation) that may connect between the aorta on the front and the left subclavian artery posteriorly going to the left arm.

During development of aortic arch, if the proximal portion of the right fourth arch disappears instead of distal portion, the right subclavian artery will arise as the last branch of aortic arch. It then courses behind the esophagus (or rarely in front of esophagus, or even in front of trachea) to supply blood to right arm. This causes pressure on esophagus and results in dysphagia. It can sometimes result in upper gastrointestinal tract bleeding.

Preauricular sinuses and cysts result from developmental defects of the first and second pharyngeal arches. This and other congenital ear malformations are sometimes associated with renal anomalies. They may be present in Beckwith–Wiedemann syndrome, and in rare cases, they may be associated with branchio-oto-renal syndrome.

Dysphagia lusoria (or Bayford-Autenrieth dysphagia) is abnormal condition characterized by difficulty in swallowing caused by aberrant right subclavian artery. It was discovered by David Bayford in 1761 and first reported in a paper by the same in 1787.

The most common symptom of laryngotracheal stenosis is gradually-worsening breathlessness (dyspnea) particularly when undertaking physical activities (exertional dyspnea). The patient may also experience added respiratory sounds which in the more severe cases can be identified as stridor but in many cases can be readily mistaken for wheeze. This creates a diagnostic pitfall in which many patients with laryngotracheal stenosis are incorrectly diagnosed as having asthma and are treated for presumed lower airway disease. This increases the likelihood of the patient eventually requiring major open surgery in benign disease and can lead to tracheal cancer presenting too late for curative surgery to be performed.

Laryngotracheal stenosis refers to abnormal narrowing of the central air passageways. This can occur at the level of the larynx, trachea, carina or main bronchi.

In a small number of patients narrowing may be present in more than one anatomical location.

Occasionally a preauricular sinus or cyst can become infected.

Most preauricular sinuses are asymptomatic, and remain untreated unless they become infected too often. Preauricular sinuses can be excised with surgery which, because of their close proximity to the facial nerve, is performed by an appropriately trained, experienced surgeon (e.g. a specialist General Surgeon, a Plastic Surgeon, an otolaryngologist (Ear, Nose, Throat surgeon) or an Oral and Maxillofacial Surgeon).

The clinical presentation of HFM is quite variable. The severity may depend on the extent of the area with an insufficient blood supply "in utero", and the gestational age of the fetus at which this occurs. In some people, the only physical manifestation may be a small and underdeveloped external ear. In more severe cases, multiple parts of the face may be affected. Some people with HFM may have sensorineural hearing loss and decreased visual acuity or even blindness.

Goldenhar syndrome can be thought of as a particularly severe form of HFM, in which extracranial anomalies are present to some extent. Some of the internal organs (especially the heart, kidneys, and lungs) may be underdeveloped, or in some cases even absent altogether. The affected organs are typically on the same side as the affected facial features, but bilateral involvement occurs in approximately 10% of cases. Deformities of the vertebral column such as scoliosis may also be observed in Goldenhar syndrome.

While there is no universally accepted grading scale, the OMENS scale (standing for Orbital, Mandible, Ear, Nerves and Soft tissue) was developed to help describe the heterogeneous phenotype that makes up this sequence or syndrome.

Intellectual disability is not typically seen in people with HFM.

Double aortic arch (DAA) is a relatively rare congenital cardiovascular malformation. DAA is an of the aortic arch in which two aortic arches form a complete vascular ring that can compress the trachea and/or esophagus. Most commonly there is a larger (dominant) right arch behind and a smaller (hypoplastic) left aortic arch in front of the trachea/esophagus. The two arches join to form the descending aorta which is usually on the left side (but may be right-sided or in the midline). In some cases the end of the smaller left aortic arch closes (left atretic arch) and the vascular tissue becomes a fibrous cord. Although in these cases a complete ring of two patent aortic arches is not present, the term ‘vascular ring’ is the accepted generic term even in these anomalies.

The symptoms are related to the compression of the trachea, esophagus or both by the complete vascular ring. Diagnosis can often be suspected or made by chest x-ray, barium esophagram, or echocardiography. Computed tomography (CT) or magnetic resonance imaging (MRI) show the relationship of the aortic arches to the trachea and esophagus and also the degree of tracheal narrowing. Bronchoscopy can be useful in internally assessing the degree of tracheomalacia. Treatment is surgical and is indicated in all symptomatic patients. In the current era the risk of mortality or significant morbidity after surgical division of the lesser arch is low. However, the preoperative degree of tracheomalacia has an important impact on postoperative recovery. In certain patients it may take several months (up to 1–2 years) for the obstructive respiratory symptoms (wheezing) to disappear.

The three most common symptoms of Opitz G/BBB syndrome (both type I & II) are hypertelorism (exceptionally wide-spaced eyes), laryngo-tracheo-esophalgeal defects (including clefts and holes in the palate, larynx, trachea and esophagus) and hypospadias (urinary openings in males not at the tip of the penis) (Meroni, Opitz G/BBB syndrome, 2012). Abnormalities in the larynx, trachea and esophagus can cause significant difficulty breathing and/or swallowing and can result in reoccurring pneumonia and life-threatening situations. Commonly, there may be a gap between the trachea and esophagus, referred to as a laryngeal cleft; which can allow food or fluid to enter the airway and make breathing and eating a difficult task.

Genital abnormalities like a urinary opening under the penis (hypospadias), undescended testes (cryptorchidism), underdeveloped scrotum and a scrotum divided into two lobes (bifid scrotum) can all be commonplace for males with the disease.

Developmental delays of the brain and nervous system are also common in both types I and II of the disease. 50% of people with Opitz G/BBB Syndrome will experience developmental delay and mild intellectual disability. This can impact motor skills, speech and learning capabilities. Some of these instances are likened to autistic spectrum disorders. Close to half of the people with Opitz G/BBB Syndrome also have a cleft lip (hole in the lip opening) and possibly a cleft palate (hole in the roof of the mouth), as well. Less than half of the people diagnosed have heart defects, imperforate anus (obstructed anal opening), and brain defects. Of all the impairments, female carriers of X-linked Type I Opitz G/BBB Syndrome usually only have ocular hypertelorism.

Athelia is the congenital absence of one or both nipples. It is a rare condition. It sometimes occurs on one side in children with the Poland sequence and on both sides in certain types of ectodermal dysplasia.