There is still much debate to whether pulmonary sequestration is a congenital problem or acquired through reccurent pulmonary infection. It is widely believed that extralobar pulmonary sequestrations are a result of prenatal pulmonary malformation while intralobar pulmonary sequestrations can develop due to reccurent pulmonary infections in adolescents and young adults.

Failure to have a pulmonary sequestration removed can lead to a number of complications. These include:

- Hemorrhage that can be fatal.

- The creation of a left-right shunt, where blood flows in a shortcut through the feed off the aorta.

- Chronic infection. Diseases such as bronchiectasis, tuberculosis, aspergillosis, bronchial carcinoid and bronchogenic squamous cell carcinoma.

It is most commonly caused by:

- Oesophageal rupture, for example in Boerhaave syndrome

- Asthma or other conditions leading to alveolar rupture

- Bowel rupture, where air in the abdominal cavity tracts up into the chest.

It has also been associated with:

- "Mycoplasma pneumoniae" pneumonia

- obesity

It can be induced to assist thoracoscopic surgery. It can be caused by a pulmonary barotrauma resulting when a person moves to or from a higher pressure environment, such as when a SCUBA diver, a free-diver or an airplane passenger ascends or descends.

In rare cases, pneumomediastinum may also arise as a result of blunt chest trauma (e.g. car accidents, fights, over pressure of breathing apparatus), while still evolving in the same fashion as the spontaneous form.

Pneumomediastinum is most commonly seen in otherwise healthy young male patients and may not be prefaced by a relevant medical history of similar ailments.

In most cases, a fetus with CPAM is closely monitored during pregnancy and the CPAM is removed via surgery after birth. Most babies with a CPAM are born without complication and are monitored during the first few months. Many patients have surgery, typically before their first birthday, because of the risk of recurrent lung infections associated with CPAMs. Some pediatric surgeons can safely remove these lesions using very tiny incisions using minimally invasive surgical techniques (thoracoscopy). However, some CPAM patients live a full life without any complication or incident. It is hypothesized that there are thousands of people living with an undetected CPAM. Through ultrasound testing employed in recent years, many more patients are aware that they live with this condition. Rarely, long standing CPAMs have been reported to become cancerous.

Very large cystic masses might pose a danger during birth because of the airway compression. In this situation, a special surgical type of delivery called the EXIT procedure may be used.

In rare extreme cases, where fetus's heart is in danger, fetal surgery can be performed to remove the CPAM. If non-immune hydrops fetalis develop, there is a near universal mortality of the fetus without intervention. Fetal surgery can improve the chances of survival to 50-60%. Recently, several studies found that a single course of prenatal steroids (betamethasone) may increase survival in hydropic fetuses with microcystic CPAMs to 75-100%. These studies indicate that large microcystic lesions may be treated prenatally without surgical intervention. Large macrocyst lesions may require in utero placement of a Harrison thoracoamniotic shunt.

With liver transplantation, the 5 year survival rate is 74%, which is comparable to patients who undergo liver transplants who do not suffer from hepatopulmonary syndrome.

Pulmonary diseases may also impact newborns, such as pulmonary hyperplasia, pulmonary interstitial emphysema (usually preterm births), and infant respiratory distress syndrome,

Respiratory disease is a common and significant cause of illness and death around the world. In the US, approximately 1 billion "common colds" occur each year. A study found that in 2010, there were approximately 6.8 million emergency department visits for respiratory disorders in the U.S. for patients under the age of 18. In 2012, respiratory conditions were the most frequent reasons for hospital stays among children.

In the UK, approximately 1 in 7 individuals are affected by some form of chronic lung disease, most commonly chronic obstructive pulmonary disease, which includes asthma, chronic bronchitis and emphysema.

Respiratory diseases (including lung cancer) are responsible for over 10% of hospitalizations and over 16% of deaths in Canada.

In 2011, respiratory disease with ventilator support accounted for 93.3% of ICU utilization in the United States.

In medicine, hepatopulmonary syndrome is a syndrome of shortness of breath and hypoxemia (low oxygen levels in the blood of the arteries) caused by vasodilation (broadening of the blood vessels) in the lungs of patients with liver disease. Dyspnea and hypoxemia are worse in the upright position (which is called platypnea and orthodeoxia, respectively).

Congenital pulmonary airway malformation (CPAM), formerly known as congenital cystic adenomatoid malformation (CCAM), is a congenital disorder of the lung similar to bronchopulmonary sequestration. In CPAM, usually an entire lobe of lung is replaced by a non-working cystic piece of abnormal lung tissue. This abnormal tissue will never function as normal lung tissue. The underlying cause for CPAM is unknown. It occurs in approximately 1 in every 30,000 pregnancies.

In most cases the outcome of a fetus with CPAM is very good. In rare cases, the cystic mass grows so large as to limit the growth of the surrounding lung and cause pressure against the heart. In these situations, the CPAM can be life-threatening for the fetus. CPAM can be separated into five types, based on clinical and pathologic features. CPAM type 1 is the most common, with large cysts and a good prognosis. CPAM type 2 (with medium-sized cysts) often has a poor prognosis, owing to its frequent association with other significant anomalies. Other types are rare.

Pneumomediastinum (from Greek "pneuma" – "air", also known as mediastinal emphysema) is (abnormal presence of air or other gas) in the mediastinum. First described in 1819 by René Laennec, the condition can result from physical trauma or other situations that lead to air escaping from the lungs, airways, or bowel into the chest cavity.

According to a study in cyanotic congenital heart disease (CCHD) in Sohag University, Upper Egypt. 50 neonates were diagnosed as suffering from cyanotic congenital heart disease (CCHD), they concluded that cyanotic congenital heart disease (CCHD) frequency was significant (9.5%) with D-TGA being the commonest type. Majority of neonates with Cyanotic congenital heart disease (CCHD) showed survival with suitable management.

Cyanotic heart defect is a group-type of congenital heart defect (CHD) that occurs due to deoxygenated blood bypassing the lungs and entering the systemic circulation or a mixture of oxygenated and unoxygenated blood entering the systemic circulation. It is caused by structural defects of the heart (i.e.: right-to-left, bidirectional shunting, malposition of the great arteries), or any condition which increases pulmonary vascular resistance. The result being the development of collateral circulation.

Congenital cysts of the larynx with incidence of about 1.8 in 100,000 newborns.

Laryngeal cysts form 4% of all laryngeal tumors or about 5% of benign laryngeal lesions. Prevalence is about equal between the sexes.

Congenital hepatic fibrosis is an inherited fibrocystic liver disease associated with proliferation of interlobular bile ducts within the portal areas and fibrosis that do not alter hepatic lobular architecture. The fibrosis would affect resistance in portal veins leading to portal hypertension.

Studies suggest that prenatal care for mothers during their pregnancies can prevent congenital amputation. Knowing environmental and genetic risks is also important. Heavy exposure to chemicals, smoking, alcohol, poor diet, or engaging in any other teratogenic activities while pregnant can increase the risk of having a child born with a congenital amputation. Folic acid is a multivitamin that has been found to reduce birth defects.

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.

The condition is usually congenital, but sporadic cases have also been reported. It may be associated with other congenital defects, commonly with autosomal recessive polycystic kidney disease, the most severe form of PKD. Some suggest that these two conditions are one disorder with different presentation.

The presence of rheumatoid arthritis alters how a person's immune system responds to foreign materials, such as dust from a coal mine. When a person with rheumatoid arthritis is exposed to such offensive materials, they are at an increased risk of developing pneumoconiosis.

Caplan syndrome occurs only in patients with both RA and pneumoconiosis related to mining dust (coal, asbestos, silica). The condition occurs in miners (especially those working in anthracite coal-mines), asbestosis, silicosis and other pneumoconioses. There is probably also a genetic predisposition, and smoking is thought to be an aggravating factor.

The epidemiology of pulmonary valve stenosis can be summed up by the congenital aspect which is the majority of cases, in broad terms PVS is rare in the general population.

The exact cause of congenital amputation is unknown and can result from a number of causes. However, most cases show that the first three months in a pregnancy are when most birth defects occur because that is when the organs of the fetus are beginning to form. One common cause is amniotic band syndrome, which occurs when the inner fetal membrane (amnion) ruptures without injury to the outer membrane (chorion). Fibrous bands from the ruptured amnion float in the amniotic fluid and can get entangled with the fetus, thus reducing blood supply to the developing limbs to such an extent that the limbs can become strangulated; the tissues die and are absorbed into the amniotic fluid. A baby with congenital amputation can be missing a portion of a limb or the entire limb, which results in the complete absence of a limb beyond a certain point where only a stump is left is known as transverse deficiency or amelia. When a specific part is missing, it is referred to as longitudinal deficiency. Finally, phocomelia occurs when only a mid-portion of a limb is missing; for example when the hands or feet are directly attached to the trunk of the body.

Amnion ruptures can be caused by:

- teratogenic drugs (e.g. thalidomide, which causes phocomelia), or environmental chemicals

- ionizing radiation (atomic weapons, radioiodine, radiation therapy)

- infections

- metabolic imbalance

- trauma

Congenital amputation is the least common reason for amputation, but it is projected that one in 2000 babies are born each year with a missing or deformed limb. During certain periods in history, an increase in congenital amputations has been documented. One example includes the thalidomide tragedy that occurred in the 1960s when pregnant mothers were given a tranquilizer that contained the harmful drug, which produced an increase in children born without limbs. Another example was the 1986 Chernobyl catastrophe in Ukraine, where the radiation exposure caused many children to be born with abnormal or missing limbs .

There are three types of laryngeal cysts, namely, mucous, hemorrhagic and congenital. However, a new classification system for congenital laryngeal cysts on the basis of the extent of the cyst and the embryologic tissue of origin, is proposed for the ease of initial surgical management.

Large and especially giant congenital nevi are at higher risk for malignancy degeneration into melanoma. Because of the premalignant potential, it is an acceptable clinical practice to remove congenital nevi electively in all patients and relieve the nevocytic overload.

This condition has been linked to mutations in the ribosomal GTPase BMS1 gene.

Shunting refers to blood that bypasses the pulmonary circulation, meaning that the blood does not receive oxygen from the alveoli. In general, a shunt may be within the heart or lungs, and cannot be corrected by administering oxygen alone. Shunting may occur in normal states:

- Anatomic shunting, occurring via the bronchial circulation, which provides blood to the tissues of the lung. Shunting also occurs by the smallest cardiac veins, which empty directly into the left ventricle.

- Physiological shunts, occur due to the effect of gravity. The highest concentration of blood in the pulmonary circulation occurs in the bases of the pulmonary tree compared to the highest pressure of gas in the apexes of the lungs. Alveoli may not be ventilated in shallow breathing.

Shunting may also occur in disease states:

- Acute lung injury and adult respiratory distress syndrome, which may cause alveolar collapse. This will increase the amount of physiological shunting, and unlike many forms of shunting, can be managed by administering 100% Oxygen.

- Pathological shunts such as patent ductus arteriosus, patent foramen ovale, and atrial septal defects or ventricular septal defects. These states are when blood from the right side of the heart moves straight to the left side, without first passing through the lungs. This is known as a right-to-left shunt, which is often congenital in origin.