Although this is a congenital lesion, airway sounds typically begin at age 4–6 weeks. Until that age, inspiratory flow rates may not be high enough to generate the sounds. Symptoms typically peak at age 6–8 months and remit by age 2 years.

Late-onset laryngomalacia may be a distinct entity, which can present after age of 2 years

Although laryngomalacia is not associated with a specific gene, there is evidence that some cases may be inherited. Relaxation or a lack of muscle tone in the upper airway may be a factor. It is often worse when the infant is on his or her back, because the floppy tissues can fall over the airway opening more easily in this position.

There are three types of tracheomalacia:

- Type 1—congenital, sometimes associated with tracheoesophageal fistula or esophageal atresia

- Type 2—extrinsic compression sometimes due to vascular rings

- Type 3—acquired due to chronic infection or prolonged intubation or inflammatory conditions like relapsing polychondritis

Tracheomalacia is a condition where the cartilage that keeps the airway (trachea) open is soft such that the trachea partly collapses especially during increased airflow. The usual symptom is stridor when a person breathes out.

The trachea normally opens slightly during breathing in and narrows slightly during breathing out. These processes are exaggerated in tracheomalacia, leading to airway collapse on breathing out.

If the condition extends further to the large airways (bronchi) (if there is also bronchomalacia), it is termed tracheobronchomalacia. The same condition can also affect the larynx, which is called laryngomalacia. The term is from "trachea" and the Greek μαλακία, "softening"

LPR is often regarded as a subtype of GERD that occurs when stomach contents flow upward through the esophagus and reach the level of the larynx and pharynx. However, LPR is associated with a distinct presentation of symptoms. LPR and GERD frequently differ in the relative prevalence of heartburn and throat clearing. While heartburn is present in over 80% of GERD cases, it occurs in only 20% of LPR cases. Throat clearing shows the opposite prevalence pattern, occurring in approximately 87% of LPR cases and in fewer than 5% of GERD cases. Unlike GERD, LPR also poses a risk for bronchitis or pneumonitis as reflux of stomach acid to the level of the larynx can result in aspiration. LPR is also commonly associated with erythema, or redness, as well as edema in the tissues of the larynx that are exposed to gastric contents. In contrast, most cases of GERD are nonerosive, with no apparent injury to the mucosal lining of the esophageal tissue exposed to the refluxed material.

Differences in the molecular structure of the epithelial tissue lining the laryngopharyngeal region may be partly responsible for the different symptomatic manifestations of LPR in comparison to GERD. In contrast to the resistant stratified squamous epithelium lining the esophagus, the larynx is lined by ciliated respiratory epithelium, which is more fragile and susceptible to damage. While the epithelium lining the esophagus is capable of withstanding as many as 50 instances of exposure to gastric contents each day, which is the uppermost estimate considered to be within the range of normal physiologic functioning, injury to laryngeal epithelium can occur following exposure to only small amounts of acidic gastric contents.

LPR was not discussed as a separate condition from GERD until the 1970s and 1980s. However, at around the same time that GERD was first recognized as a clinical entity in the mid-1930s, a link between gut symptoms and airway disease was suggested. Later, acid-related laryngeal s and granulomas were reported in 1968. Subsequent studies suggested that acid reflux might be a contributory factor in other laryngeal and respiratory conditions. In 1979, the link between these airway symptoms and reflux of gastric contents was first documented. At the same time, treatment of reflux disease results was shown to eliminate these airway symptoms.

Subglottic stenosis is a congenital or acquired narrowing of the subglottic airway. Although it is relatively rare, it is the third most common congenital airway problem (after laryngomalacia and vocal cord paralysis). Subglottic stenosis can present as a life-threatening airway emergency. It is imperative that the otolaryngologist be an expert at dealing with the diagnosis and management of this disorder. Subglottic stenosis can affect both children and adults.

Subglottic stenosis can be of three forms, namely congenital subglottic stenosis, idiopathic subglottic stenosis (ISS) and acquired subglottic stenosis. As the name suggests, congenital subglottic stenosis is a birth defect. Idiopathic subglottic stenosis is a narrowing of the airway due to an unknown cause. Acquired subglottic stenosis generally follows as an after-effect of airway intubation, and in extremely rare cases as a result of gastroesophageal reflux disease (GERD).

Subglottic stenosis is graded according to the Cotton-Meyer classification system from one to four based on the severity of the blockage.

Grade 1 – <50% obstruction

Grade 2 – 51–70% obstruction

Grade 3 – 71–99% obstruction

Grade 4 – no detectable lumen

Treatments to alleviate the symptoms of subglottic stenosis includes a daily dose of steroids such as prednisone, which reduces the inflammation of the area for better breathing. Other medications such as Methotrexate is also being tested by patients but results are pending.

A vascular ring is a congenital defect in which there is an abnormal formation of the aorta and/or its surrounding blood vessels. The trachea and esophagus are completely encircled and sometimes compressed by a "ring" formed by these vessels, which can lead to breathing and digestive difficulties.

Most often this is because of persistence of the double aortic arch after the second month of fetal life.

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.

Genitopatellar Syndrome is an autosomal dominant inheritance where the mutation in the KAT6B causes the syndrome. The KAT6B gene is responsible for making an enzyme called histone acetyltransferase which functions in regulating and making of histone which are proteins that attach to DNA and give the chromosomes their shape. The function of histone acetyltransferase produced from KAT6B is unknown but it is considered as a regulator of early developments. There is little known about how the mutation in the KAT6B causes the syndrome but researchers suspects that the mutations occur near the end of the KAT6B gene and causes it to produce shortened acetyltransferase enzyme. The shortened enzyme alters the regulation of other genes. On the other hand, the mutation of KAT6B leading to the specific features of genitopatellar syndrome is still not surely proven.

Genitopatellar syndrome is a rare disorder with characteristic craniofacial features, congenital flexion contractures of the lower limbs, absent or abnormal patellae, urogenital anomalies, and severe psychomotor retardation.

In 2012, it was shown that mutations in the gene KAT6B cause the syndrome.

Inflammation occurs in the laryngeal, tracheal and bronchial cartilages. Both of these sites are involved in 10% of persons with RP at presentation and 50% over the course of this autoimmune disease, and is more common among females.

The involvement of the laryngotracheobronchial cartilages may be severe and life-threatening; it causes one-third of all deaths among persons with RP.

Laryngeal chondritis is manifested as pain above the thyroid gland and, more importantly, as dysphonia with a hoarse voice or transient aphonia. Because this disease is relapsing, recurrent laryngeal inflammation may result in laryngomalacia or permanent laryngeal stenosis with inspiratory dyspnea that may require emergency tracheotomy as a temporary or permanent measure.

Tracheobronchial involvement may or may not be accompanied with laryngeal chondritis and is potentially the most severe manifestation of RP.

The symptoms consist of dyspnea, wheezing, a nonproductive cough, and recurrent, sometimes severe, lower respiratory tract infections.

Obstructive respiratory failure may develop as the result of either permanent tracheal or bronchial narrowing or chondromalacia with expiratory collapse of the tracheobronchial tree. Endoscopy, intubation, or tracheotomy has been shown to hasten death.

Relapsing polychondritis is an autoimmune disease in which the body's immune system begins to attack and destroy the cartilage tissues in the body. It has been postulated that both cell-mediated immunity and humoral immunity are responsible.

Reasons for disease onset are not known, but there is no evidence of a genetic predisposition to developing relapsing polychondritis. However, there are cases where multiple members of the same family have been diagnosed with this illness. Studies indicate that some genetic contribution to susceptibility is likely.

Fetal warfarin syndrome (dysmorphism due to warfarin, warfarin embryopathy) is a condition associated with administration of warfarin during pregnancy.

Associated conditions include hypoplasia of nasal bridge, laryngomalacia, pectus carinatum, congenital heart defects, ventriculomegaly, agenesis of the corpus callosum, stippled epiphyses, telebrachydactyly, and growth retardation.

It is also known as "DiSaia syndrome". The symptoms are nasal hypoplasia, depressed nasal bridge, deep groove between nostril and nasal tip, stippling of uncalcified epiphyses during first year, mild hypoplasia of nails, shortened fingers, low birth weight, significant intellectual disability, seizures, reduced muscle tone, widely spaced nipples, deafness and feeding difficulty.