Gastroesophageal reflux disease (GERD) affects approximately 40% of adults. Strictures occur in 7 to 23% of patients with GERD who are untreated.

Neonates with TEF or esophageal atresia are unable to feed properly. Once diagnosed, prompt surgery is required to allow the food intake. Some children do experience problems following TEF surgery; they can develop dysphagia and thoracic problems. Children with TEF can also be born with other abnormalities, most commonly those described in VACTERL association - a group of anomalies which often occur together, including heart, kidney and limb deformities. 6% of babies with TEF also have a laryngeal cleft.

About 6 to 14 percent of patients who receive a routine barium swallow test of the esophagus are found to have a Schatzki ring.

The thyroglossal tract arises from the foramen cecum at the junction of the anterior two-thirds and posterior one-third of the tongue. Any part of the tract can persist, causing a sinus, fistula or cyst. Most fistulae are acquired following rupture or incision of the infected thyroglossal cyst. A thyroglossal cyst is lined by pseudostratified, ciliated columnar epithelium while a thyroglossal fistula is lined by columnar epithelium.

Thyroglossal Duct Cysts are a birth defect. During embryonic development, the thyroid gland is being formed, beginning at the base of the tongue and moving towards the neck canal, known as the thyroglossal duct. Once the thyroid reaches its final position in the neck, the duct normally disappears. In some individuals, portions of the duct remain behind, leaving small pockets, known as cysts. During a person's life, these cyst pockets can fill with fluids and mucus, enlarging when infected, presenting the thyroglossal cyst.

Zenker's diverticulum mainly affects older adults. It has an incidence of 2 per 100,000 per year in the UK, but there is significant geographical variation around the world.

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

In simple words, when there is excessive pressure within the lower pharynx, the weakest portion of the pharyngeal wall balloons out, forming a diverticulum which may reach several centimetres in diameter.

More precisely, while traction and pulsion mechanisms have long been deemed the main factors promoting development of a Zenker's diverticulum, current consensus considers occlusive mechanisms to be most important: uncoordinated swallowing, impaired relaxation and spasm of the cricopharyngeus muscle lead to an increase in pressure within the distal pharynx, so that its wall herniates through the point of least resistance (known as Killian's triangle, located superior to the cricopharyngeus muscle and inferior to the Thyropharyngeus muscle. Thyropharyngeus and Laryngopharyngeus are the superior and inferior parts of inferior constrictor muscle of pharynx respectively). The result is an outpouching of the posterior pharyngeal wall, just above the esophagus.

While it may be asymptomatic, Zenker diverticulum can present with the following symptoms:

- Dysphagia (difficulty swallowing), and sense of a lump in the throat

- Food might get trapped in the outpouching, leading to:

- Regurgitation, reappearance of ingested food in the mouth

- Cough, due to food regurgitated into the airway

- Halitosis, smelly breath, as stagnant food is digested by microorganisms

- Infection

It rarely, if ever, causes any pain.

Cervical webs are seen associated in 50% of patients with this condition.

Rarer forms of cervical esophageal diverticula are the Killian's diverticulum and the Laimer's diverticulum. Killian's diverticulum is formed in the Killian-Jamiseon triangle (located inferior to the cricopharyngeus on both sides of this muscle's insertion into the cricoid cartilage). Laimer's diverticulum is formed in Laimer's triangle (located inferior to the cricopharyngeus in the posterior midline above the confluence of the longitudinal layer of esophageal muscle). Laimer's triangle is covered only by the circular layer of esophageal muscle.

A cyst is a closed sac, having a distinct membrane and division compared with the nearby tissue. Hence, it is a cluster of cells that has grouped together to form a sac (not unlike the manner in which water molecules group together, forming a bubble); however, the distinguishing aspect of a cyst is that the cells forming the "shell" of such a sac are distinctly abnormal (in both appearance and behaviour) when compared with all surrounding cells for that given location. It may contain air, fluids, or semi-solid material. A collection of pus is called an abscess, not a cyst. Once formed, sometimes a cyst may resolve on its own. When a cyst fails to resolve, it may need to be removed surgically, but that would depend upon its type and location.

Cancer-related cysts are formed as a defense mechanism for the body, following the development of mutations that lead to an uncontrolled cellular division. Once that mutation has occurred, the affected cells divide incessantly (and become known as cancerous), forming a tumour. The body encapsulates those cells to try to prevent them from continuing their division and to try to contain the tumour, which becomes known as a cyst. That said, the cancerous cells still may mutate further and gain the ability to form their own blood vessels, from which they received nourishment before being contained. Once that happens, the capsule becomes useless and the tumour may advance from benign to a cancer.

Some cysts are neoplastic and thus, are called cystic tumors; many types are not neoplastic. Some are dysplastic or metaplastic. Pseudocysts are similar to cysts (having a sac filled with fluid), but lack an epithelial lining.

Two percent of women will have a Bartholin's gland cyst at some point in their lives. They occur at a rate of 0.55 per 1000 person-years and in women aged 35–50 years at a rate of 1.21 per 1000 person-years. The incidence of Bartholin duct cysts increases with age until menopause, and decreases thereafter. Hispanic women may be more often affected than white women and black women. The risk of developing a Bartholin's gland cyst increases with the number of childbirths.

While Bartholin cysts can be quite painful, they are not life-threatening. New cysts cannot absolutely be prevented from forming, but surgical or laser removal of a cyst makes it less likely that a new one will form at the same site. Those with a cyst are more likely than those without a cyst to get one in the future. They can recur every few years or more frequently. Many women who have marsupialization done find that the recurrences may slow, but do not actually stop.

It can be caused by or associated with gastroesophageal reflux disease, esophagitis, a dysfunctional lower esophageal sphincter, disordered motility, lye ingestion, or a hiatal hernia. Strictures can form after esophageal surgery and other treatments such as laser therapy or photodynamic therapy. While the area heals, a scar forms, causing the tissue to pull and tighten, leading to difficulty in swallowing.

Blocked sebaceous glands, swollen hair follicles, high levels of testosterone and the use of androgenic anabolic steroids will cause such cysts.

A case has been reported of a sebaceous cyst being caused by the human botfly.

Hereditary causes of sebaceous cysts include Gardner's syndrome and basal cell nevus syndrome.

Esophageal rupture in Boerhaave syndrome is thought to be the result of a sudden rise in internal esophageal pressure produced during vomiting, as a result of neuromuscular incoordination causing failure of the cricopharyngeus muscle (a sphincter within the esophagus) to relax. As the intra-oesophageal pressure increases, the bolus within the oesophagus has nowhere to go superiorly (as the cricopharyngeus fails to relax) which causes the oesophagus to rupture. (this makes little sense and should be justified if true: the lesion is down, the cricopharyngeus is up). The syndrome is commonly associated with the consumption of excessive food and/or alcohol as well as eating disorders such as bulimia.

The most common anatomical location of the tear in Boerhaave syndrome is at left posterolateral wall of the lower third of the esophagus, 2–3 cm before the stomach.

Currently, the most common cause of esophageal perforation is iatrogenic. However, iatrogenic perforations, while still constituting a serious medical condition, are easier to treat and less prone to complications, particularly mediastinitis and sepsis. This is because they usually do not involve contamination of the mediastinum with gastric contents.

Many CNS cysts form in the womb during the first few weeks of development as a result of congenital defects. In adults cysts may also form due to a head injury or trauma, resulting in necrotic tissues (dead tissue), and can sometimes be associated with cancerous tumors or infection in the brain. However, the underlying reasons for cyst formation are still unknown.

With the exception of a few case reports describing survival without surgery, the mortality of untreated Boerhaave syndrome is nearly 100%. Its treatment includes immediate antibiotic therapy to prevent mediastinitis and sepsis, surgical repair of the perforation, and if there is significant fluid loss it should be replaced with IV fluid therapy since oral rehydration is not possible. Even with early surgical intervention (within 24 hours) the risk of death is 25%.

Esophageal diseases can derive from congenital conditions, or they can be acquired later in life.

Many people experience a burning sensation in their chest occasionally, caused by stomach acids refluxing into the esophagus, normally called heartburn. Extended exposure to heartburn may erode the lining of the esophagus, leading potentially to Barrett's esophagus which is associated with an increased risk of adenocarcinoma most commonly found in the distal one-third of the esophagus.

Some people also experience a sensation known as globus esophagus, where it feels as if a ball is lodged in the lower part of the esophagus.

The following are additional diseases and conditions that affect the esophagus:

- Achalasia

- Acute esophageal necrosis

- Barrett's esophagus

- Boerhaave syndrome

- Caustic injury to the esophagus

- Chagas disease

- Diffuse esophageal spasm

- Esophageal atresia and Tracheoesophageal fistula

- Esophageal cancer

- Esophageal dysphagia

- Esophageal varices

- Esophageal web

- Esophagitis

- GERD

- Hiatus hernia

- Jackhammer esophagus (hypercontractile peristalsis)

- Killian–Jamieson diverticulum

- Mallory-Weiss syndrome

- Neurogenic dysphagia

- Nutcracker esophagus

- Schatzki's ring

- Zenker's Diverticulum

Cysts derived from CNS tissues are very common in America. They are a subtype of cerebrovascular diseases, which are the third leading cause of death in America. Generally, CNS cysts are present in all geographic regions, races, ages, and sexes. However, certain types of CNS cysts are more prevalent in certain types of individuals than others. Some examples of incidence rates in specific types of cysts include:

- Arachnoid cysts are more prevalent in males than females

- Colloid cysts are more prevalent in adults

- Dermoid cysts are more prevalent in children under 10 years of age

- Epidermoid cysts are more prevalent in middle-aged adults

Treatment ranges from simple enucleation of the cyst to curettage to resection. There are cysts—e.g., buccal bifurcation cyst—that resolve on their own, in which just close observation may be employed, unless it is infected and symptomatic.

Radicular cysts are by far the most common cyst occurring in the jaws.

About 90% of pilar cysts occur on the scalp, with the remaining sometimes occurring on the face, trunk and extremities. Pilar cysts are significantly more common in females, and a tendency to develop these cysts is often inherited in an autosomal dominant pattern. In most cases, multiple pilar cysts appear at once.

One proposed cause of pilonidal cysts is ingrown hair. Excessive sitting is thought to predispose people to the condition, as sitting increases pressure on the coccygeal region. Trauma is not believed to cause a pilonidal cyst; however, such an event may result in inflammation of an existing cyst. However, there are cases where this can occur months after a localized injury to the area. Some researchers have proposed that pilonidal cysts may be the result of a congenital pilonidal dimple. Excessive sweating can also contribute to the cause of a pilonidal cyst. Moisture can fill a stretched hair follicle, which helps create a low-oxygen environment that promotes the growth of anaerobic bacteria, often found in pilonidal cysts. The presence of bacteria and low oxygen levels hamper wound healing and exacerbate a forming pilonidal cyst.

The prognosis depends upon the type, size and location of a cyst. Most cysts are entirely benign, and some may require no treatment. Rarely, some cystic lesions represent locally aggressive tumors that may cause destruction of surrounding bone if left untreated. This type of cyst are usually removed with a margin of healthy bone to prevent recurrence of new cysts. If a cyst expands to a very large size, the mandible may be weakened such that a pathologic fracture occurs.

Barrett's esophagus is a premalignant condition. Its malignant sequela, oesophagogastric junctional adenocarcinoma, has a mortality rate of over 85%. The risk of developing esophageal adenocarcinoma in people who have Barrett's esophagus has been estimated to be 6–7 per 1000 person-years, however a cohort study of 11,028 patients from Denmark published in 2011 showed an incidence of only 1.2 per 1000 person-years (5.1 per 1000 person-years in patients with dysplasia, 1.0 per 1000 person-years in patients without dysplasia). The relative risk of esophageal adenocarcinoma is approximately 10 in those with Barret's esophagus, compared to the general population. Most patients with esophageal carcinoma survive less than one year.

Treatment for dermoid cyst is complete surgical removal, preferably in one piece and without any spillage of cyst contents. Marsupialization, a surgical technique often used to treat pilonidal cyst, is inappropriate for dermoid cyst due to the risk of malignancy.

The association of dermoid cysts with pregnancy has been increasingly reported. They usually present the dilemma of weighing the risks of surgery and anesthesia versus the risks of untreated adnexal mass. Most references state that it is more feasible to treat bilateral dermoid cysts of the ovaries discovered during pregnancy if they grow beyond 6 cm in diameter.