Various etiologies have been proposed, including trauma, hemorrhage, chronic infection, and mucoid degeneration. The most widely accepted theory describes meniscal cysts resulting from extrusion of synovial fluid through a peripherally extended horizontal meniscal tear, accumulating outside the joint capsule. They arise more commonly from the medial joint margin, and occur most often in 20- to 40-year-old males.

A meniscal cyst is a well-defined cystic lesion located along the peripheral margin of the meniscus, a part of the knee, nearly always associated with horizontal meniscal tears.

Recurrence rate is higher in aspirated cysts than in excised ones. Ganglion cysts have been found to recur following surgery in 12% to 41% of patients.

A six-year outcome study of the treatment of ganglion cysts on the dorsum (back) of the wrist compared excision, aspiration, and no treatment. Neither excision nor aspiration provided long-term benefit better than no treatment. Of the untreated ganglion cysts, 58% resolved spontaneously; the post-surgery recurrence rate in this study was 39%. A similar study in 2003 of ganglion cysts occurring on the palmar surface of the wrist states: "At 2 and 5 year follow-up, regardless of treatment, no difference in symptoms was found, regardless of whether the palmar wrist ganglion was excised, aspirated or left alone."

The most commonly accepted probable cause of ganglion cysts is the "herniation hypothesis", by which they are thought to occur as "an out-pouching or distention of a weakened portion of a joint capsule or tendon sheath." This description is based on the observations that the cysts occur close to tendons and joints, the microscopic anatomy of the cyst resembles that of the tenosynovial tissue, the fluid is similar in composition to synovial fluid, and dye injected into the joint capsule frequently ends up in the cyst, which may become enlarged after activity. Dye injected into the cyst rarely enters the joint, however, which has been attributed to the apparent formation of an effective and one-way "check valve", allowing fluid out of the joint, but not back in.

In synovials, posttraumatic degeneration of connective tissue and inflammation have been considered as causes. Other possible mechanisms for the development of ganglion cysts include repeated mechanical stress, facet arthrosis, myxoid degeneration of periarticular fibrous tissues and liquefaction with chronic damage, increased production of hyaluronic acid by fibroblasts, and a proliferation of mesenchymal cells. Ganglion cysts also may develop independently from a joint.

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.

A Baker's cyst, also known as a popliteal cyst, is a benign swelling of the semimembranosus or more rarely some other synovial bursa found behind the knee joint. It is named after the surgeon who first described it, William Morrant Baker (1838–1896). It is not a "true" cyst, as an open communication with the synovial sac is often maintained.

In adults, Baker's cysts usually arise from almost any form of knee arthritis (e.g., rheumatoid arthritis) or cartilage (particularly a meniscus) tear. Baker's cysts in children do not point to underlying joint disease. Baker's cysts arise between the tendons of the medial head of the gastrocnemius and the semimembranosus muscles. They are posterior to the medial femoral condyle.

The synovial sac of the knee joint can, under certain circumstances, produce a posterior bulge, into the popliteal space, the space behind the knee. When this bulge becomes large enough, it becomes palpable and cystic. Most Baker's cysts maintain this direct communication with the synovial cavity of the knee, but sometimes, the new cyst pinches off. A Baker's cyst can rupture and produce acute pain behind the knee and in the calf and swelling of the calf muscles.

Pilonidal disease is a type of skin infection which typically occurs between the cheeks of the buttocks and often at the upper end. Symptoms may include pain, swelling, and redness. There may also be drainage of fluid. It rarely results in a fever.

Risk factors include obesity, family history, prolonged sitting, greater amounts of hair, and not enough exercise. The underlying mechanism is believed to involve a mechanical process. The lesions may contains hair and skin debris. Diagnosis is based on symptoms and examination.

If there is infection, treatment is generally by incision and drainage just off the midline. Shaving the area may prevent recurrence. More extensive surgery may be required if the disease recurs. Antibiotics are generally not needed. Without treatment the condition may remain long term.

About 3 per 10,000 people are affected a year. It occurs more often in males than females. Often it occurs in young adulthood. The term means "nest of hair". It was first described in 1833.

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.

Arachnoid cysts are seen in up to 1.1% of the population with a gender distribution of 2:1 male:female Only 20% of these have symptoms, usually from secondary hydrocephalus.

A study that looked at 2,536 healthy young males found a prevalence of 1.7% (95% CI 1.2 to 2.3%). Only a small percentage of the detected abnormalities require urgent medical attention.

The clinical management of a cyst of Montgomery depends upon the symptoms of the patient.

If there are no signs of infection, a cyst of Montgomery can be observed, because more than 80% resolve spontaneously, over only a few months. However, in some cases, spontaneous resolution may take up two years. In such cases, a repeat ultrasonography may become necessary. If, however, the patient has signs of an infection, for example reddening (erythema), warmth, pain and tenderness, a treatment for mastitis can be initiated, which may include antibiotics and non-steroidal anti-inflammatory drugs (NSAIDs). With treatment, inflammatory changes usually disappear quickly. In rare cases, drainage may become necessary. A surgical treatment of a cyst of Montgomery, i.e. a resection, may become necessary only if a cyst of Montgomery persists, or the diagnosis is questioned clinically.

The prognosis seems to be excellent. In one series, all adolescent patients with a cyst of Montgomery had a favourable outcome.

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.

The nasopalatine duct cyst (abbreviated NPDC) occurs in the median of the palate, usually anterior to first molars. It often appears between the roots of the maxillary central incisors. Radiographically, it may often appear as a heart-shaped radiolucency. It is usually asymptomatic, but may sometimes produce an elevation in the anterior portion of the palate. It was first described by Meyer in 1914.

The median palatal cyst has recently been identified as a possible posterior version of the nasopalatine duct cyst.

There is not a specific theory behind the etiology of the unicameral bone cyst, however, according to many researchers and doctors, there is a commonly known theory hypothesized by Jonathan Cohen in 1970. Cohen studied interstitial fluid in six children undergoing treatment for unicameral bone cysts. He believed that the chemical composition of the fluid found in the bone cyst was similar to the chemical make-up in serum. Cohen theorized that the unicameral bone cyst occurs when interstitial fluids in cancellous bones quickly accumulate in one region from blockage.

One of the other theories is that the cysts result from a disorder of the growth plate. Another is that the cysts result from problems with circulation that are caused by a developmental anomaly in the veins of the affected bone. The role trauma plays in the development of these cysts is unknown. Some speculate that repeated trauma puts the bone at risk for developing a bone cyst. This, however, has not been proven.

The exact cause of arachnoid cysts is not known. Researchers believe that most cases of arachnoid cysts are developmental malformations that arise from the unexplained splitting or tearing of the arachnoid membrane.

In some cases, arachnoid cysts occurring in the middle fossa are accompanied by underdevelopment (hypoplasia) or compression of the temporal lobe. The exact role that temporal lobe abnormalities play in the development of middle fossa arachnoid cysts is unknown.

There are some cases where hereditary disorders have been connected with arachnoid cysts.

Some complications of arachnoid cysts can occur when a cyst is damaged because of minor head trauma. Trauma can cause the fluid within a cyst to leak into other areas (e.g., subarachnoid space). Blood vessels on the surface of a cyst may tear and bleed into the cyst (intracystic hemorrhage), increasing its size. If a blood vessel bleeds on the outside of a cyst, a collection of blood (hematoma) may result. In the cases of intracystic hemorrhage and hematoma, the individual may have symptoms of increased pressure within the cranium and signs of compression of nearby nerve (neural) tissue.

Some scientists debate whether arachnoid cysts are a true congenite condition or if this should be separated from secondary cysts. A recent study shows differences in communication between the arachnoid cyst and the subarachnoid space by CT cisternography

. A comparison of arachnoid cyst fluid and CSF in a series of patients show differences in chemical composition.

Arachnoid cysts can also occur secondary to other disorders such as Marfan syndrome, arachnoiditis, or agenesis of the corpus callosum.

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.

About 25% of people over the age of 50 experience knee pain from degenerative knee diseases.

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

Although the treatment of the cyst was previously enuclation of the cyst with removal of the involved tooth or enuclation with root-canal treatment, the current management is enuclation with the preservation of the involved tooth. However, recent evidence suggests self-resolution of this type of cyst, thus close observation with meticulous oral hygiene measures can be employed unless the cyst is infected and symptomatic.

A urachal cyst is a sinus remaining from the allantois during embryogenesis. It is a cyst which occurs in the remnants between the umbilicus and bladder. This is a type of cyst occurring in a persistent portion of the urachus, presenting as an extraperitoneal mass in the umbilical region. It is characterized by abdominal pain, and fever if infected. It may rupture, leading to peritonitis, or it may drain through the umbilicus. Urachal cysts are usually silent clinically until infection, calculi or adenocarcinoma develop.

Buccal bifurcation cyst is an inflammatory odontogenic cyst, of the paradental cysts family, that typically appears in the buccal bifurcation region of the mandibular first molars in the second half of the first decade of life. Infected cysts may be associated with pain.

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.

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

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.