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.

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.

A sinus tract, or small channel, may originate from the source of infection and open to the surface of the skin. Material from the cyst may drain through the pilonidal sinus. A pilonidal cyst is usually painful, but with draining, the patient might not feel pain.

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.

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.

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.

Oral mucocele (also termed mucous retention cyst, mucous extravasation cyst, mucous cyst of the oral mucosa, and mucous retention and extravasation phenomena) is a clinical term that refers to two related phenomena:

- Mucus extravasation phenomenon

- Mucus retention cyst

The former is a swelling of connective tissue consisting of a collection of fluid called mucin. This occurs because of a ruptured salivary gland duct usually caused by local trauma (damage), in the case of mucus extravasation phenomenon, and an obstructed or ruptured salivary duct (parotid duct) in the case of a mucus retention cyst. The mucocele has a bluish translucent color, and is more commonly found in children and young adults.

Although the term cyst is often used to refer to these lesions, mucoceles are not strictly speaking true cysts because there is no epithelial lining. Rather, it would be more accurate to classify mucoceles as polyps (i.e. a lump).

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.

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.

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."

Epidermoid cysts commonly result from implantation of epidermis into the dermis, as in trauma or surgery. They can also be caused by a blocked pore adjacent to a body piercing. They are also seen in Gardner's syndrome and Nevoid Basal Cell Carcinoma Syndrome on the head and neck. They can be infected by bacteria and form a pimple-like shape.

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.

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.

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 epidermoid cyst may have no symptoms, or it may hurt when touched. It can release pus. It is very common for women on the major or minor labia. In contrast to pilar cysts, epidermoid cysts are usually present on parts of the body with relatively little hair.

Occasionally, an epidermoid cyst will present with Trigeminal neuralgia.

Although they are not malignant, there are rare cases of malignant tumors arising from an epidermoid cyst.

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.

The nasopalatine cyst is the most common non-odontogenic cyst of the oral cavity, at an estimated occurrence rate of 73%.

A thyroglossal duct cyst may rupture unexpectedly, resulting in a draining sinus known as a thyroglossal fistula. Thyroglossal fistula can develop when the removal of the cyst has not been fully completed. This is usually noticed when bleeding in the neck occurs, causing swelling and fluid ejection around the original wound of removal.

It is estimated that 7% of women in the western world develop palpable breast cysts.

There is preliminary evidence that women with breast cysts may be at an increased risk of breast cancer, especially at younger ages.

In males, the occurrence of breast cysts is rare and may (but need not) be an indication of malignancy.

Nabothian cysts are considered harmless and usually disappear on their own, although some will persist indefinitely. Some women notice they appear and disappear in relation to their menstrual cycle. If a woman is not sure the anomaly she has found on her cervix is a nabothian cyst, a visit to a doctor is recommended to rule out other conditions.

Rarely, nabothian cysts have a correlation with chronic cervicitis, an inflammatory infection of the cervix.

Nabothian cysts are not considered problematic unless they grow very large and present secondary symptoms. A physician may wish to perform a colposcopy or biopsy on a nabothian cyst to check for cancer or other problems. Two methods for removing these cysts include electrocautery and cryofreezing, although new cysts may form after the procedure.

Both mucous retention and extravasation phenomena are classified as salivary gland disorders.

The periareolar glands of Montgomery in the breast are also called Montgomery tubercles or Morgagni tubercles. These periareolar glands are small, papular tissue projections at the edge of the areola (nipple).

Obstruction of the Montgomery tubercles may result in an acute inflammation, a clear or light brownish fluid may drain out of the areola (nipple discharge), and an subareolar mass may develop, the cyst of Montgomery.

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.