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.

Diaphragmatic injuries are present in 1–7% of people with significant blunt trauma and an average of 3% of abdominal injuries.

A high body mass index may be associated with a higher risk of diaphragmatic rupture in people involved in vehicle accidents. It is rare for the diaphragm alone to be injured, especially in blunt trauma; other injuries are associated in as many as 80–100% of cases. In fact, if the diaphragm is injured, it is an indication that more severe injuries to organs may have occurred. Thus, the mortality after a diagnosis of diaphragmatic rupture is 17%, with most deaths due to lung complications. Common associated injuries include head injury, injuries to the aorta, fractures of the pelvis and long bones, and lacerations of the liver and spleen. Associated injuries occur in over three quarters of cases.

A significant complication of diaphragmatic rupture is traumatic diaphragmatic herniation: organs such as the stomach that herniate into the chest cavity and may be strangulated, losing their blood supply. Herniation of abdominal organs is present in 3–4% of people with abdominal trauma who present to a trauma center.

Lung hernia (Sibson hernia) is a protrusion of lung outside of thoracic wall. In 20% patients with lung hernia, the incidence is congenital. In 80% of the cases, the hernia is noted after chest trauma, thoracic surgery or certain pulmonary diseases. Congenital hernia occurs because of the weakness of the suprapleural membrane or neck muscles. In pulmonary diseases such as asthma, frequent coughing can lead to high intra thoracic pressure, causing the lung to herniate out. Lung hernia may occur near the neck (cervical), between the ribs (intercostal), near the vertebrae (paravertebral) or near the sternum (parasternal).

No treatment is needed for correcting lung hernias. Some surgeons offer cosmetic surgery to remove the protruding mass.

For individuals who survive the initial crush injury, survival rates are high for traumatic asphyxia.

A hemothorax is a type of pleural effusion in which blood accumulates in the pleural cavity. This excess fluid can interfere with normal breathing by limiting the expansion of the lungs. The term is from "" + "thorax".

Causes of pulmonary hypoplasia include a wide variety of congenital malformations and other conditions in which pulmonary hypoplasia is a complication. These include congenital diaphragmatic hernia, congenital cystic adenomatoid malformation, fetal hydronephrosis, caudal regression syndrome, mediastinal tumor, and sacrococcygeal teratoma with a large component inside the fetus. Large masses of the neck (such as cervical teratoma) also can cause pulmonary hypoplasia, presumably by interfering with the fetus's ability to fill its lungs. In the presence of pulmonary hypoplasia, the EXIT procedure to rescue a baby with a neck mass is not likely to succeed.

Fetal hydrops can be a cause, or conversely a complication.

Pulmonary hypoplasia is associated with oligohydramnios through multiple mechanisms. Both conditions can result from blockage of the urinary bladder. Blockage prevents the bladder from emptying, and the bladder becomes very large and full. The large volume of the full bladder interferes with normal development of other organs, including the lungs. Pressure within the bladder becomes abnormally high, causing abnormal function in the kidneys hence abnormally high pressure in the vascular system entering the kidneys. This high pressure also interferes with normal development of other organs. An experiment in rabbits showed that PH also can be caused directly by oligohydramnios.

Pulmonary hypoplasia is associated with dextrocardia of embryonic arrest in that both conditions can result from early errors of development, resulting in Congenital cardiac disorders.

PH is a common direct cause of neonatal death resulting from pregnancy induced hypertension.

Pulmonary hypoplasia is incomplete development of the lungs, resulting in an abnormally low number or size of bronchopulmonary segments or alveoli. A congenital malformation, it most often occurs secondary to other fetal abnormalities that interfere with normal development of the lungs. Primary (idiopathic) pulmonary hypoplasia is rare and usually not associated with other maternal or fetal abnormalities.

Incidence of pulmonary hypoplasia ranges from 9–11 per 10,000 live births and 14 per 10,000 births. Pulmonary hypoplasia is a relatively common cause of neonatal death. It also is a common finding in stillbirths, although not regarded as a cause of these.

Bochdalek hernias make up about 0.17% to 6% of all diaphragmatic hernia cases and about one in every 2200 to 12,500 births every year. Babies who are born with a Bochdalek hernia are more than likely to have another birth defect caused by the hernia. About twenty percent of those children born with a Bochdalek hernia, also have a congenital heart defect. In addition, infants born with this condition may also have other abnormalities. "Between five and sixteen [percent of infants] have a chromosomal abnormality." In most cases, left-sided hernias or Bochdalek hernias have a ratio of 3:2 of males to females. In other words, Bochdalek hernias are more common in men.

The death rate of people with flail chest depends on the severity of their condition, ranging from 10 to 25%.

The mediastinum (from Medieval Latin "mediastinus", "midway") is the central compartment of the thoracic cavity surrounded by loose connective tissue, as an undelineated region that contains a group of structures within the thorax. The mediastinum contains the heart and its vessels, the esophagus, trachea, phrenic and cardiac nerves, the thoracic duct, thymus and lymph nodes of the central chest.

Bochdalek hernia can be a life-threatening condition. Approximately 85.3% of newborns born with a Bochdalek hernia are immediately high risk. Infants born with a Bochdalek hernia have a "high mortality rate due to respiratory insufficiency". Between 25–60% of infants with a Bochdalek hernia die. The lungs, diaphragm, and digestive system are all forming at the same time, so when a Bochdalek hernia permits the abdominal organs to invade the chest cavity rather than remain under the diaphragm in the correct position, it puts the infant in critical condition. These "foreign bodies" in the chest cavity compress the lungs, impairing their proper development and causing pulmonary hypoplasia. Since the lungs of infants suffering from a Bochdalek hernia have fewer alveoli than normal lungs, Bochdalek hernias are life-threatening conditions due to respiratory distress. Also, if the invasion of the intestine or stomach punctures the lung, then the lungs cannot fill completely with air. The baby will not be healthy or stable with this condition because he or she cannot take in enough air and oxygen to keep the body operating properly. Like the lungs, the intestines may also have trouble developing correctly. If the intestines are trapped within the lungs, then the lungs and intestines may not be receiving the amount of blood they need to stay healthy and function properly.

Its cause is usually traumatic, from a blunt or penetrating injury to the thorax, resulting in a rupture of the serous membrane either lining the thorax or covering the lungs. This rupture allows blood to spill into the pleural space, equalizing the pressures between it and the lungs. Blood loss may be massive in people with these conditions, as each side of the thorax can hold 30 to 40% of a person's blood volume or 1.5 to 2 L per side in the average adult. Even minor injury to the chest wall can lead to significant hemothorax.

Less frequently, hemothorax occurs spontaneously. A major vascular cause of hemothorax is aortic dissection or rupture of thoracic aortic aneurysms. It may also follow surgical intervention in the thoracic area. Infrequently, patients with pneumothorax may develop spontaneous hemothorax. Spontaneous hemothorax or hemopneumothorax may be occur with endometriosis, if endometrial tissue implants on the pleural surface, then bleeds in response to cyclical hormonal changes in menstruating women.

The sudden impact on the thorax causes an increase in intrathoracic pressure. In order for traumatic asphyxia to occur, a Valsalva maneuver is required when the traumatic force is applied. Exhalation against the closed glottis along with the traumatic event causes air that cannot escape from the thoracic cavity. Instead, the air causes increased venous back-pressure, which is transferred back to through the right atrium, to the superior vena cava and to the head and neck veins and capillaries.

Approximately 1 out of 13 people admitted to the hospital with fractured ribs are found to have flail chest.

The cause of IPF is unknown but certain environmental factors and exposures have been shown to increase the risk of getting IPF. Cigarette smoking is the best recognized and most accepted risk factor for IPF, and increases the risk of IPF by about twofold. Other environmental and occupation exposures such as exposure to metal dust, wood dust, coal dust, silica, stone dust, biologic dusts coming from hay dust or mold spores or other agricultural products, and occupations related to farming/livestock have also been shown to increase the risk for IPF. There is some evidence that viral infections may be associated with idiopathic pulmonary fibrosis and other fibrotic lung diseases.

In some cases (particularly where whole litters are affected) FCKS can be due to genetic factors: certain bloodlines are known to produce a preponderance of kittens with the condition, and close matings very commonly produce it in the offspring. Isolated cases are more likely due to environmental factors or slight prematurity of the kittens concerned, and even complete litters suffering from FCKS may have no genetic component—repeat matings that have produced flat kittens in one instance have often not produced it again, and recovered FCKS that have been bred from have likewise not necessarily produced offspring that suffered from the condition.

IPF has been recognized in several breeds of both dogs and cats, and has been best characterized in West Highland White Terriers. Veterinary patients with the condition share many of the same clinical signs as their human counterparts, including progressive exercise intolerance, increased respiratory rate, and eventual respiratory distress.

Prognosis is generally poor.

The occurrence of ectopia cordis is 8 per million births. It is typically classified according to location of the ectopic heart, which includes:

- Cervical

- Thoracic

- Thoracoabdominal

- Abdominal

Thoracic and thoraco-abdominal ectopia cordis constitute the vast majority of known cases.

Ectopia cordis (Greek: ""away / out of place"" + Latin: ""heart"") is a congenital malformation in which the heart is abnormally located either partially or totally outside of the thorax. The ectopic heart can be found along a spectrum of anatomical locations, including the neck, chest, or abdomen. In most cases, the heart protrudes outside the chest through a split sternum.

A kitten that has difficulty in breathing is very likely also to suffer from colic (which can cause weight loss in the early development of a normal kitten), and a very small daily (or twice daily) dose of liquid paraffin (one or two drops placed on the tongue of the kitten, or 0.1 ml) should help to alleviate this problem. FCKS kittens who do not maintain weight are usually among the group which die, but many of them may simply be unable to feed properly due to colic, becoming increasingly weak and lethargic, and fading due to malnutrition as much as to the thoracic problems.

Colic has many causes, but in a kitten with respiratory difficulty it is possible that a malfunction during the breathing process leads the kitten to swallow air instead of taking it into its lungs. The GI tract fills with air while the lungs do not receive a proper air supply, preventing them from inflating fully. Pressure from the stomach exacerbates the condition. Treating for colic with liquid paraffin seems to shorten recovery time from 4–10 weeks to a matter of days.

The most widely accepted pathophysiological mechanism by which Chiari type I malformations occur is by a reduction or lack of development of the posterior fossa as a result of congenital or acquired disorders. Congenital causes include hydrocephalus, craniosynostosis (especially of the lambdoid suture), hyperostosis (such as craniometaphyseal dysplasia, osteopetrosis, erythroid hyperplasia), X-linked vitamin D-resistant rickets, and neurofibromatosis type I. Acquired disorders include space occupying lesions due to one of several potential causes ranging from brain tumors to hematomas.

Head trauma may cause cerebellar tonsillar ectopia, possibly because of dural strain. Additionally, ectopia may be present but asymptomatic until whiplash causes it to become symptomatic. Posterior fossa hypoplasia causes reduced cerebral and spinal compliance.

The condition is rare but serious, and appears in all mammals. It results from leakage of lymph fluid from the thoracic duct (or one of its tributaries). This can result from direct laceration (e.g., from surgery) or from nontraumatic causes. The most common nontraumatic cause is malignancy, especially lymphoma. Less common is left-heart failure, infections, and developmental abnormalities such as Down syndrome and Noonan syndrome.