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.

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

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.

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.

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.

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.

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.

The lateral periodontal cyst is a non-inflammatory developmental cyst that arises from the epithelial post-functional dental lamina, which is a remnant from odontogenesis. It is more common in middle-aged males. Usually asymptomatic, it presents as a regular well-corticated radiolucency on the side of a mandibular canine or premolar root. Histologically, the cyst appears similar to the gingival cyst of the adult, having a non-keratinized squamous epithelial lining. The involved tooth is usually vital and has no indication for root canal treatment unless the signs of non-vital or necrotic pulpal tissue were confirmed. The cysts arise from epithelial rest cells in the periodontal ligament, although it is unknown whether from the cell rests of Malassez, reduced enamel epithelium or dental lamina remnants, and are generally treated by surgical enucleation.

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.

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.

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.

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.

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 median alveolar cyst is a rare cyst, occurring in the bony alveolus between the maxillary central incisors. It is distinguished from a periapical cyst by the fact that adjacent teeth are vital.

Some mucoceles spontaneously resolve on their own after a short time. Others are chronic and require surgical removal. Recurrence may occur, and thus the adjacent salivary gland is excised as a preventive measure.

Several types of procedures are available for the surgical removal of mucoceles. These include laser and minimally-invasive techniques which means recovery times are reduced drastically.

Micro-marsupialization is an alternative procedure to surgical removal. Micro-marsupialization uses silk sutures in the dome of a cyst to allow new epithelialized drainage pathways. It is simpler, less traumatic, and well-tolerated by patients, especially children.

A non-surgical option that may be effective for a small or newly identified mucocele is to rinse the mouth thoroughly with salt water (one tablespoon of salt per cup) four to six times a day for a few days. This may draw out the fluid trapped underneath the skin without further damaging the surrounding tissue. If the mucocele persists, individuals should see a doctor to discuss further treatment.

Smaller cysts may be removed by laser treatment, larger cysts will have to be removed surgically in an operating room.

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 .

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.

Gingival cyst of adult is a rare condition. The incidence is less than 0.5%. It is formed from the rests of dental lamina. It is found in the soft tissues on the buccal and labial portions of the jaw. It usually occurs on the facial gingiva as a single small flesh colored swelling, sometimes with a bluish hue due to the cystic fluid. Sometimes, it may occur in cluster, either unilaterally or bilaterally or on the lingual surface of the alveolar process. It is most commonly seen in the canine and premolar regions of the mandible, and are sometimes confused with lateral periodontal cysts. It is not normally problematic, but when it grows larger, it can cause some discomfort. It can be removed by simple surgical excision. They are developed late in life, generally up to the sixth decade of age.

Treatment options include antibiotic therapy (not a permanent solution), endodontic (root canal) therapy, or extraction.

Paradental cysts constitute a family of inflammatory odontogenic cyst, that typically appear in relation to crown or root of partially erupted molar tooth. When the cyst is developed in the distal region of partially erupted third molar or in other locations in the dentition, it called simply "paradental cyst", but the unique cyst that developed in the buccal bifurcation region of the mandibular first molars in the second half of the first decade of life is called buccal bifurcation cyst and has unique clinical features and management considerations in comparison to the other paradental cysts.

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.

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.

Treatment may include antibiotic therapy, hot compresses and application of depilatory creams. In more severe cases, the cyst may need to be lanced or treated surgically. Lancing is performed using a local anesthesia, with healing time generally under one week. The most conservative surgical treatment, Bascom's Pit Picking procedure, is a relatively simple outpatient option that can be performed in a physician's office, involves minimal pain and requires only a few days healing. Although this procedure is much less invasive than the alternatives, it is not regularly practiced in the US. The Pit Picking procedure provides good results, fast recovery, and in instances where it is unsuccessful, other options for more invasive surgery can still be performed.

The more common course for surgical treatment is for the cyst to be surgically excised (along with pilonidal sinus tracts). Post-surgical wound packing may be necessary, and packing typically must be replaced once daily for 4 to 8 weeks. In some cases, two years may be required for complete granulation to occur. Sometimes the cyst is resolved via surgical marsupialization.

Surgeons can also excise the sinus and repair with a reconstructive flap technique, such as a "cleft lift" procedure or Z-plasty, usually done under general anesthetic. This approach is especially useful for complicated or recurring pilonidal disease, leaves little scar tissue and flattens the region between the buttocks, reducing the risk of recurrence. This approach typically results in a more rapid recovery than the traditional surgery, however there are fewer surgeons trained in the cleft lift procedure and thus, it may not be as accessible to patients, depending on their geographic location. Meta analysis shows recurrence rates were lower in open healing than with primary closure (RR 0.60, 95% CI 0.42 to 0.87) at the expense of time to healing. Pilonidal cysts recur and do so more frequently if the surgical wound is sutured in the midline, as opposed to away from the midline, which obliterates the natal cleft and removes the focus of shearing stress. An incision lateral to the intergluteal cleft is therefore preferred, especially given the poor healing of midline incisions in this region.

An attractive minimally invasive technique is to treat pilonidal sinus with fibrin glue. This technique is less painful than traditional excisional techniques and flaps, can be performed under local or general anaesthesia, does not require dressings or packing and allows return to normal activities within 1 to 2 days. Long term outcome and recurrence rates are not dissimilar to more invasive techniques in 5 year follow up in a small randomised controlled trial.

Fibrin glue has also been shown to be better than more invasive alternatives in the treatment of pilonidal sinus disease in children, where a quick return to normal activities and minimal postoperative pain are especially important.

A minimally invasive surgical technique, was developed in Israel by Moshe Gips et al.,2008. and is similar to the pit picking technique first described by Bascom in 1980 In this procedure, trephines or biopsy punches which only "core out" and remove the diseased tissue and cyst are used, leaving only small holes to heal. Work or school activities will be resumed in one or two days, without or with minimal postoperative pain. The two procedures have been successfully combined by L. Basso in Rome (Italy).

While the recovery rate is positive for most, some suffer long term effects. Recorded instances include patients with continued postoperative pain for years following the surgical procedure. Primary complaints included pain when sitting for long period of times or following abrasive contact with the lower back and buttocks.

A dentigerous cyst or follicular cyst is an odontogenic cyst - thought to be of developmental origin - associated with the crown of an unerupted (or partially erupted) tooth. The cyst cavity is lined by epithelial cells derived from the reduced enamel epithelium of the tooth forming organ. Regarding its pathogenesis, it has been suggested that the pressure exerted by an erupting tooth on the follicle may obstruct venous flow inducing accumulation of exudate between the reduced enamel epithelium and the tooth crown.

In addition to the developmental origin, some authors have suggested that periapical inflammation of non-vital deciduous teeth in proximity to the follicles of unerupted permanent successors may be a factor for triggering this type of cyst formation.

Histologically a normal dental follicle is lined by enamel epithelium, whereas a dentigerous cyst is lined by non-keratinized stratified squamous epithelium. Since the dentigerous cyst develops from follicular epithelium it has more potential for growth, differentiation and degeneration than a radicular cyst. Occasionally the wall of a dentigerous cyst may give rise to a more ominous mucoepidermoid carcinoma. Due to the tendency for dentigerous cysts to expand rapidly, they may cause pathological fractures of jaw bones.

On Fine needle aspiration, thin straw colored fluid is seen.

The usual radiographic appearance is that of a well-demarcated radiolucent lesion attached at an acute angle to the cervical area of an unerupted tooth. The border of the lesion may be radiopaque. The radiographic differentiation between a dentigerous cyst and a normal dental follicle is based merely on size. Radiographically, a dentigerous cyst should always be differentiated from a normal dental follicle. Dentigerous cysts are the most common cysts with this radiographic appearance. Radiographically the cyst appears unilocular with well defined margins and often sclerotic borders but sometimes it may be multilocular in appearance and may also have a continuous cystic membrane. Infected cysts show ill-defined margins. Follicular space more than 3mm is to be considered a dentigerous cyst.

Radiographically there are three types of dentigerous cyst, namely the Central type, Lateral type and the Circumferential type.

The most common location of dentigerous cysts are the Mandibular 3rd Molars and the Maxillary Canines, and they rarely involve deciduous teeth and are occasionally associated with odontomas.

A dentigerous cyst is often treated by excision of the cyst along with the extraction of the associated tooth.

In case of a large cyst marsupialization is done.

An eruption cyst, or eruption hematoma, is a bluish swelling that occurs on the soft tissue over an erupting tooth. It is usually found in children. The fluid in the cyst is sometimes clear creating a pale-coloured cyst although often they are blue. An eruption cyst (eruption hematoma) is a developmental soft-tissue cyst of odontogenic origin that forms over an erupting tooth.