Smaller lesions can be followed expectantly. Larger lesions, lesions that are growing or symptomatic, and lesions with sonographically suspicious findings (septation, papillations, fluid and solid components) are generally surgically explored and removed.

The diagnostic process typically begins with a medical history workup followed by a medical examination by a physician. Imaging tests, such as CT scans and MRIs, help provide a clearer picture. The physician typically looks for fluid (or other bodily substance) filled sacs to appear in the scans, as is shown in the CT scan of a colloid cyst. A primary health care provider will refer an individual to a neurologist or neurosurgeon for further examination. Other diagnostic methods include radiological examinations and macroscopic examinations. After a diagnosis has been made, immunohistochemistry may be used to differentiate between epithelial cysts and arachnoid cysts. These examinations are useful to get a general idea of possible treatment options, but can be unsatisfactory to diagnose CNS cysts. Professionals still do not fully understand how cysts form; however, analyzing the walls of different cyst types, using electron microscopes and light microscopes, has proven to be the best diagnostic tool. This has led to more accurate cyst classification and correct course of action for treatments that are cyst specific. In the past, before imaging scans or tests were available, medical professionals could only diagnose cysts via exploratory surgery.

A small dermoid cyst on the coccyx can be difficult to distinguish from a pilonidal cyst. This is partly because both can be full of hair. A pilonidal cyst is a pilonidal sinus that is obstructed. Any teratoma near the body surface may develop a sinus or a fistula, or even a cluster of these. Such is the case of Canadian Football League linebacker Tyrone Jones, whose teratoma was discovered when he blew a tooth out of his nose.

Epidermoid cysts are usually diagnosed when a person notices a bump on their skin and seeks medical attention. The definitive diagnosis is made after excision by a pathologist based on microscopic appearance of a cystic lesion lined by cornified epithelium containing lamellated keratin without calcifications. They can also be seen as isointense lesions on MRI or hyperintensities on FLAIR.

The cystic nature of a breast lump can be confirmed by ultrasound examination, aspiration (removal of contents with needle), or mammogram. Ultrasound can also show if the cyst contains solid nodules, a sign that the lesion may be pre-cancerous or cancerous. Examination by a cytopathologist of the fluid aspirated from the cyst may also help with this diagnosis. In particular, it should be sent to a laboratory for testing if it is blood-stained.

Commonly, cysts are detected with the help of mammograms. However, the medical history and physical examination also play an important role in establishing an accurate diagnosis. During these tests, the doctor will try to find out as much information as possible regarding the symptoms the patient has experienced, their intensity and duration and the physical examination is performed regularly to check for other abnormalities that may exist within the breast.

As mentioned above, cysts are often undetectable at touch. Therefore, a mammogram can provide valuable and clear images of the breast tissue. Generally, if there is any abnormality within the breast tissue, it will be shown on the mammogram. There are two types of mammograms available. One of them is primarily used in screening, and are ordered for patients who do not show any symptoms and these are called screening mammograms. Diagnostic mammograms are used on patients who developed certain symptoms of a breast condition or in patients whose screening mammograms showed abnormalities.

Patients suspected of breast cysts will normally be given a diagnosing mammogram, although they are not suspected of cancer. This type of mammogram provides the doctor with the possibility of performing a breast ultrasound at the same time and this is the reason why they are often preferred over the screening mammograms. Breast ultrasound is considered the best option when diagnosing breast cysts because it is 95 to 100% accurate, it provides a clear image on the cyst's appearance (simple or complex) and it may also distinguish between solid lumps and fluid-filled cysts, which a mammogram cannot do. Breast ultrasounds are performed with the help of a handheld medical instrument which is placed on the skin, after a special type of fluid has been applied on it. The instruments picks up the echo resulted from the sound waves it sends to the breast. These echoes are transmitted to a computer which translates it into a picture.

Breast cysts may remain stable for many years or may resolve spontaneously. Most simple cysts are benign and do not require any treatment or further diagnostic workup. Some complex cysts may require further diagnostic measures such as fine needle aspiration or biopsy to exclude breast cancer however the overwhelming majority is of benign nature. Aspiration both diagnoses and removes cysts at the same time. That is, cysts will usually resolve on their own after the fluid is drained. Otherwise, if the lump is not a cyst, the fluid aspirated may contain blood or there may not be fluid at all. Whereas in the first case, the fluid is sent to the laboratory for further examination, the latter circumstance is a sign that the breast lump is solid. This type of tumor needs to be biopsied in order to determine whether it is malignant or benign.

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.

A cyst of Montgomery may be asymptomatic. Yet, a cyst of Montgomery usually is diagnosed when a female patient, 10–20 years of age, complains to a healthcare professional of breast pain (mastalgia), inflammation or a palpable nodule in the breast. The diagnosis is made clinically, when a palpable nodule is felt in the retroareolar area.

The diagnosis can be confirmed with ultrasonography, frequently showing a simple cyst in the retroareolar area. In some patients, multiple cysts or bilateral cysts may exist. Cysts of Montgomery may have liquid content with an echogenic or calcific sediment.

PTCs are generally benign, but may, on rare occasions, give rise to borderline tumors and malignancies.

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.

Ovarian cysts are usually diagnosed by ultrasound, CT scan, or MRI, and correlated with clinical presentation and endocrinologic tests as appropriate.

Most cysts are discovered as a chance finding on routine dental radiography. On an x-ray, cysts appear as radiolucent (dark) areas with radiopaque (white) borders. Cysts are usually unilocular, but may also be multilocular. Sometimes aspiration is used to aid diagnosis of a cystic lesion, e.g. fluid aspirate from a radicular cyst may appear straw colored and display shimmering due to cholesterol content. Almost always, the cyst lining is sent to a pathologist for histopathologic examination after it has been surgically removed. This means that the exact diagnosis of the type of cyst is often made in retrospect.

Follow-up imaging in women of reproductive age for incidentally discovered simple cysts on ultrasound is not needed until 5 cm, as these are usually normal ovarian follicles. Simple cysts 5 to 7 cm in premenopausal females should be followed yearly. Simple cysts larger than 7 cm require further imaging with MRI or surgical assessment. Because they are large, they cannot be reliably assessed by ultrasound alone because it may be difficult to see the soft tissue nodularity or thickened septation at their posterior wall due to limited penetrance of the ultrasound beam. For the corpus luteum, a dominant ovulating follicle that typically appears as a cyst with circumferentially thickened walls and crenulated inner margins, follow up is not needed if the cyst is less than 3 cm in diameter. In postmenopausal patients, any simple cyst greater than 1 cm but less than 7 cm needs yearly follow-up, while those greater than 7 cm need MRI or surgical evaluation, similar to reproductive age females.

For incidentally discovered dermoids, diagnosed on ultrasound by their pathognomonic echogenic fat, either surgical removal or yearly follow up is indicated, regardless of patient age. For peritoneal inclusion cysts, which have a crumpled tissue-paper appearance and tend to follow the contour of adjacent organs, follow up is based on clinical history. Hydrosalpinx, or fallopian tube dilation, can be mistaken for an ovarian cyst due to its anechoic appearance. Follow-up for this is also based on clinical presentation.

For multiloculate cysts with thin septation less than 3 mm, surgical evaluation is recommended. The presence of multiloculation suggests a neoplasm, although the thin septation implies that the neoplasm is benign. For any thickened septation, nodularity, or vascular flow on color doppler assessment, surgical removal should be considered due to concern for malignancy.

A pilonidal cyst can resemble a dermoid cyst, a kind of teratoma (germ cell tumor). In particular, a pilonidal cyst in the gluteal cleft can resemble a sacrococcygeal teratoma. Correct diagnosis is important because all teratomas require complete surgical excision, if possible without any spillage, and consultation with an oncologist.

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.

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.

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.

Clinical features can be found in the subhyoid portion of the tract and 75% present as midline swellings. The remainder can be found as far lateral as the lateral tip of the hyoid bone.

Typically, the cyst will move upwards on protrusion of the tongue, given its attachment to the embryonic duct, as well as on swallowing, due to attachment of the tract to the foramen caecum.

Diagnosis of a thyroglossal duct cyst requires a medical professional, and is usually done by a physical examination. It is important to identify whether or not the thyroglossal cyst contains any thyroid tissue, as it can define the degree of cyst that is being dealt with.

Diagnostic procedures for a thyroglossal cyst include:

Colloid cysts can be diagnosed by symptoms presented. Additional testing will be required and the colloid cyst symptoms can resemble those of other diseases. MRI and CT scans are often used to confirm diagnosis.

Other conditions that may present similarly include hidradenoma papilliferum, lipomas, epidermoid cysts and Skene's duct cysts among others. In those who are more than 40 years of age a biopsy may be recommended to ensure cancer is not present.

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 is often largely dependent on the type of cyst. Asymptomatic cysts, termed pseudocysts, normally require active monitoring with periodic scans for future growth. Symptomatic (producing or showing symptoms) cysts may require surgical removal if they are present in areas where brain damage is unavoidable, or if they produce chronic symptoms disruptive to the quality of life of the patient. Some examples of cyst removal procedures include: permanent drainage, fenestration, and endoscopic cyst fenestration.

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.

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.

A small cyst that requires magnification to be seen, may be called a microcyst. Similarly, a cyst that is larger than usual or compared to others, may be called a macrocyst.