When treatment is required, this is usually by surgical removal of the cyst. There are four ways in which cysts are managed:

- Enucleation - removal of the entire cyst

- Marsupialization - the creation of a window into the wall of a cyst, allowing the contents to be drained. The window is left open, and the lack of pressure within the cyst causes the lesion to shrink, as the surrounding bone starts to fill in again.

- Enucleation following marsupialization - Sometimes marsupialization is carried out as a single procedure, but usually it is followed by a second procedure to remove the cyst. This is particularly the case when cysts are very large and their removal would leave a significant surgical defect.

- Enucleation with curettage - this is removal of the cyst and some of the surrounding bone, which may contain some of the lining of the 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.

Cysts can be removed by excision.

In case of fronto-ethmoidal epidermoid cysts, surgical resection appears to be the mainstay of treatment; however, the extent of resection is dictated by adherence of the tumor capsule to the surrounding vital structures.

Hydrogen peroxide gel (HO) was previously recommended for cyst treatment, particularly those on body piercings. However the gel cannot adequately permeate the cyst and was not found to be effective. Hydrogen peroxide is no longer recommended for wound care by doctors as it can damage the healing tissues.

On body piercings, self treatment with a hot saline soak to help drain the cyst and the use of an antibacterial or medicated talcum powder (Use of talc is no longer recommended due to recently discovered associations with multiple cancers.) to help dry out the bump and reduce bacterial proliferation is generally recommended until medical advice can be obtained. Piercings, however, are more likely to be victims of hypertrophic scarring than a cyst. Cheek piercings seem to be the piercing most prone to cysts due to the possible interruption of saliva ducts.

Treatment ranges from simple enucleation of the cyst to curettage to resection. For example, small radicular cyst may resolved after successful endodontic ("root-canal") treatment. Because of high recurrence potential and aggressive behaviour, curettage is recommended for keratocyst. However, the conservative enucleation is the treatment of choice for most odontogenic cysts. The removed cyst must be evaluated by pathologist to confirm the diagnosis, and to rule out other neoplastic lesions with similar clinical or radiographic features (e.g., cystic or solid ameloblastoma, central mucoepidermoid carcinoma). There are cysts, e.g. buccal bifurcation cyst with self-resolation nature, in which close observation can be employed unless the cyst is infected and symptomatic.

Sebaceous cysts generally do not require medical treatment. However, if they continue to grow, they may become unsightly, painful, infected, or all of the above.

Surgical excision of a sebaceous cyst is a simple procedure to completely remove the sac and its contents.

There are three general approaches used: traditional wide excision, minimal excision, and punch biopsy excision.

The typical outpatient surgical procedure for cyst removal is to numb the area around the cyst with a local anaesthetic, then to use a scalpel to open the lesion with either a single cut down the center of the swelling, or an oval cut on both sides of the centerpoint. If the cyst is small, it may be lanced instead. The person performing the surgery will squeeze out the keratin surrounding the cyst, then use blunt-headed scissors or another instrument to hold the incision wide open while using fingers or forceps to try to remove the cyst intact. If the cyst can be removed in one piece, the "cure rate" is 100%. If, however, it is fragmented and cannot be entirely recovered, the operator may use curettage (scraping) to remove the remaining exposed fragments, then burn them with an electro-cauterization tool, in an effort to destroy them in place. In such cases the cyst may recur. In either case, the incision is then disinfected and, if necessary, the skin is stitched back together over it. A scar will most likely result.

An infected cyst may require oral antibiotics or other treatment before or after excision. If pus has already formed then incision and drainage should be done along with avulsion of cyst wall with proper antibiotics coverage.

An approach involving incision, rather than excision, has also been proposed.

The infected tissue of the periapical cyst must be entirely removed, including the epithelium of the cyst wall; otherwise a relapse is likely to occur. Root canal treatment should be performed on the tooth if it is determined that previous therapy was unsuccessful. Removal of the necrotic pulp and the inflamed tissue as well as proper sealing of the canals and an appropriately fitting crown will allow the tooth to heal under uninfected conditions.

Surgical options for previously treated teeth that would not benefit from root canal therapy include cystectomy and cystostomy. This route of treatment is recommended upon discovery of the cyst after inadequate root canal treatment. A cystectomy is the removal of a cyst followed by mucosa and wound closure to reduce chances of cyst regeneration. This type of treatment is more ideal for small cysts.

A cystostomy is recommended for larger cysts that compromise important adjacent anatomy. The cyst is tamponaded to allow for the cyst contents to escape the bone. Over time, the cyst decreases in size and bone regenerates in the cavity space.

Marsupialization could also be performed, which involves suturing the edges of the gingiva surrounding the cyst to remain open. The cyst then drains its contents and heal without being prematurely closed. The end result is the same as the cystostomy, bone regeneration. For both a cystostomy and marsupialization, root resectioning may also be required in cases where root resorption has occurred.

A primordial cyst is a developmental odontogenic cyst. It is found in an area where a tooth should have formed but is missing. Primordial cysts most commonly arise in the area of mandibular third molars. Under microscopes, the cyst looks like an odontogenic keratocyst (also called a Keratocyst odontogenic tumor) whereby the lesions displays a parakeratinized epithelium with palisading basal epithelial cells.

The term "Primordial cyst" is considered an outdated term and should be avoided. Most "primordial cysts" are actually Keratocyst odontogenic tumors (KOT's).

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.

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.

Surgical excision is required to treat a trichilemmal cyst. The method of treatment varies depending on the physician's training. Most physicians perform the procedure under local anesthetic. Others prefer a more conservative approach. This involves the use of a small punch biopsy about 1/4 the diameter of the cyst. The punch biopsy is used to enter the cyst cavity. The content of the cyst is emptied, leaving an empty sac. As the pilar cyst wall is the thickest and most durable of the many varieties of cysts, it can be grabbed with forceps and pulled out of the small incision. This method is best performed on cysts larger than a pea which have formed a thick enough wall to be easily identified after the sac is emptied. Small cysts have walls that are thin, and easily fragmented on traction. This increases the likelihood of cyst recurrence. This method often results in only a small scar, and very little if any bleeding.

Odontogenic cyst are a group of jaw cysts that are formed from tissues involved in odontogenesis (tooth development). Odontogenic cysts are closed sacs, and have a distinct membrane derived from rests of odontogenic epithelium. It may contain air, fluids, or semi-solid material. Intra-bony cysts are most common in the jaws, because the mandible and maxilla are the only bones with epithelial components. That odontogenic epithelium is critical in normal tooth development. However, epithelial rests may be the origin for the cyst lining later.

Not all oral cysts are odontogenic cyst. For example, mucous cyst of the oral mucosa and nasolabial duct cyst are not of odontogenic origin.

In addition, there are several conditions with so-called (radiographic) 'pseudocystic appearance' in jaws; ranging from anatomic variants such as Stafne static bone cyst, to the aggressive aneurysmal bone cyst.

The periapical cyst (also termed radicular cyst or inflammatory cyst) is the most common odontogenic cyst. Periapical is defined as "the tissues surrounding the apex of the root of a tooth" and a cyst is "a pathological cavity lined by epithelium, having fluid or gaseous content that is not created by the accumulation of pus." Most frequently located in the maxillary anterior region, it is caused by pulpal necrosis secondary to dental caries or trauma. The cyst has lining that is derived from the epithelial cell rests of Malassez which proliferate to form the cyst. Highly common in the oral cavity, the periapical cyst is asymptomatic, but highly significant because a secondary infection can cause pain and damage. In radiographs, it appears a radiolucency (dark area) around the apex of a tooth's root.

If there is a high probability of a fracture resulting from the unicameral bone cyst, then surgical treatment is necessary. Specific methods can be determined by the physician based upon the patient’s age, medical history, tolerance for certain medical procedures or medicine, health, and extremity of the disease. The treatment can involve or incorporate one or more of the following surgical methods, which are performed by a pediatric orthopedic surgeon:

- Curettage:

- Bone Grafting:

- Steroid injection:

If a patient needs to be treated with surgery, a standard surgical procedure would be called for; the patient would be resting in Fowler’s position, a semi-sitting position, under general anesthesia. The exact size, shape, and distance between the acromion to the midpoint of the cyst are measured by a digital radiograph or MRI scan. A small, longitudinal skin incision, about 1 cm long, is made at the center of the cyst. Next, by using a trephine or drill bit, a small aperture is made inside the incision. Fluids contained in the cyst are drained and curved, metal impactors are used to break any septa, or membranes, within the cyst. Curettes are then used to remove the entire cyst from the diaphysis. After the removal of the cystic membrane, a 95% ethanol solution is injected into the cavity to produce a chemical cauterization to burn away any residual active membrane for 30 seconds and then aspirated. Saline solution is then immediately injected into the cavity to wash out any residual ethanol solution and to mitigate any damage to healthy tissue; this irrigation process of ethanol and saline solutions is repeated for another 2 to 3 times. A curved impactor is inserted into the cavity and used to penetrate the boundary between the cyst and bone marrow; the intentional penetrations will allow bone marrow cells to migrate into the cavity to produce a source of osteoinductive cells, cells that induce bony growth. Furthermore, the cavity is completely filled with bone graft substitute, such as calcium sulfate. Finally, one cannulated screw is placed into the aperture.

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.

Several synonyms exist for epidermoid cysts, including epidermal cyst, infundibular cyst, keratin cyst and the technically incorrect, epidermal inclusion cyst. "Epidermal inclusion cyst" more specifically refers to implantation of epidermal elements into the dermis. The term infundibular cyst refers to the site of origin of the cyst: the infundibular portion of the hair follicle. In fact, the majority of epidermal inclusion cysts originate from the infundibular portion of the hair follicle thus explaining the interchangeable, yet inaccurate, use of these two terms. Another similar and easily confused cyst is Sebaceous cyst.

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 glandular odontogenic cyst is a rare odontogenic cyst. In 85% of cases, it is found in the mandible, especially in anterior areas. It is more common in adults in their fifth and sixth decades. On radiographs, it can appear as a unilocular or multilocular radiolucency (dark area). Since the glandular odontogenic cyst can range in size, treatment can be as simple as enucleation and curettage to en bloc resection of the affected jaw.

The globulomaxillary cyst is a cyst that appears between a maxillary lateral incisor and the adjacent canine. It exhibits as an "inverted pear-shaped radiolucency" on radiographs, or X-ray films.

The globulomaxillary cyst often causes the roots of adjacent teeth to diverge.

This cyst should not be confused with a nasopalatine cyst.

The developmental origin has been disputed. Today, most literature agree based on overwhelming evidence that the cyst is predominantly of tooth origin (odontogenic), demonstrating findings consistent with periapical cysts, odontogenic keratocysts or lateral periodontal cysts.

Conservative (i.e. no treatment), or surgical . With surgical excision, recurrence is common, usually due to incomplete excision. Often, the tracts of the cyst will pass near important structures, such as the internal jugular vein, carotid artery, or facial nerve, making complete excision impractical.

Botryoid odontogenic cyst is a variant of the lateral periodontal cyst. It is more often found in middle-aged and older adults, and the teeth more likely affected are mandibular (lower) canines and premolars. On radiographs, the cyst appears "grape-like". Often patients with this condition are symptomatic.

Gingival cyst (or dental lamina cyst) is a type of cysts of the jaws that originates from the dental lamina and is found in the mouth parts. It is a superficial cyst in the alveolar mucosa. It can be seen inside the mouth as small and whistish bulge. Depending on the ages in which they develop, the cysts are classsfied into gingival cyst of newborn (or infant) and gingival cyst of adult. Structurally, the cyst is lined by thin epithelium and shows a lumen usually filled with desquamated keratin, occasionally containing inflammatory cells. The nodes are formes as a result of cystic degeneration of epithelial rests of the dental lamina (called the rests of Serres).

Gingival cyst was first described by a Czech physician Alois Epstein in 1880. In 1886, a German physician Heinrich Bohn described another type of cyst. Alfred Fromm introduced the classification of gingival cysts in 1967. According to him, gingival cysts of newborns can be further classsified based on their specific origin of the tissues as Epstein’s pearls, Bohn’s nodules and dental lamina cysts.

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."

Although generally benign, the cyst must be removed if the patient exhibits difficulty in breathing or swallowing, or if the cyst is infected. Even if these symptoms are not present, the cyst may be removed to eliminate the chance of infection or development of a carcinoma, or for cosmetic reasons if there is unsightly protrusion from the neck.

Thyroid scans and thyroid function studies are ordered preoperatively; this is important to demonstrate that normally functioning thyroid tissue is in its usual area.

Surgical management options include the Sistrunk procedure, en bloc central neck dissection, suture-guided transhyoid pharyngotomy, and Koempel's supra-hyoid technique. Cystectomy is an inadequate approach.

Nasopalatine duct cysts usually present as asymptomatic palatal swellings, but they may rarely be accompanied by pain and/or purulent discharge. The cysts are generally treated by .