Urethral diverticulum is often an incidental finding. It can be diagnosed using magnetic resonance imaging and/or micturating cystourethrography. Other studies that can be used to diagnose urethral diverticulum include intravenous urography, urethroscopy, and/or ultrasound. Conditions that should be distinguished from urethral diverticulum in a differential diagnosis include overactive bladder, Gartner's duct cyst, Gartner's duct abscess, ectopic caeco-ureterocele, interstitial cystitis, pelvic inflammatory disease, endometriosis, and cancer.

Ultrasound is the often chosen to examine the duct and determine the presence and size of any cysts or abnormalities. Fine-needle aspiration cytology can also be used to confirm the diagnosis.

Cysts from 1–5 mm on CT or ultrasound are typically too small to characterize and considered benign. No further imaging follow-up is recommended for these lesions. Cysts from 6–9 mm require a single follow-up in 2–3 years, preferably with MRCP to better evaluate the pancreatic duct. If stable at follow-up, no further imaging follow-up is recommended. For cysts from 1–1.9 cm follow-up is suggested with MRCP or multiphasic CT in 1–2 years. If stable at follow-up, the interval of imaging follow-up is increased to 2–3 years. Cysts from 2–2.9 cm have more malignant potential, and a baseline endoscopic ultrasound is suggested, followed by MRCP or multiphasic CT in 6–12 months. If patients are young, surgery may be considered to avoid the need for prolonged surveillance. If these cysts are stable at follow-up, interval imaging follow-up can be done in 1–2 years.

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.

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.

Diagnosis is usually made by characteristic history and physical examination. Diagnosis can be confirmed by x-ray (80% of salivary gland calculi are visible on x-ray), by sialogram, or by ultrasound.

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:

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.

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.

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.

The primary treatment for urethral diverticulum is surgical. The surgery is conducted transvaginally, usually when there is no acute inflammation to better aid dissection of the delicate tissues.

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.

Choledochal cysts are treated by surgical excision of the cyst with the formation of a roux-en-Y anastomosis hepaticojujenostomy/ choledochojujenostomy to the biliary duct.

Future complications include cholangitis and a 2% risk of malignancy, which may develop in any part of the biliary tree. A recent article published in Journal of Surgery suggested that choledochal cysts could also be treated with single-incision laparoscopic hepaticojejunostomy with comparable results and less scarring. In cases of saccular type of cyst, excision and placement of T-shaped tube is done.

Currently, there is no accepted indication for fetal intervention in the management of prenatally suspected choledochal cysts.

In order to prevent further cysts and infections from forming, the thyroglossal duct and all of its branches are removed from the throat and neck area. A procedure, known as the Sistrunk procedure, is considered to be the standard procedure and involves removal of portions of the hyoid bone and core tissue of the suprahyoid region. Cysts will often reoccur if the entire duct is not removed, so reoccurrence requires a wider range of tissue to be removed in a subsequent surgery.

Delaying the surgical procedure almost always leads to recurrent infections, which will continue to delay the needed treatment. The Sistrunk procedure has a reoccurrence rate of less than 5%, proving it is extremely effective at removing the majority of traces of the persistent thyroglossal duct.

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.

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.

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.

The most common and accurate way of diagnosing an individual with this anomaly is by MRCP (Magnetic Resonance Cholangiopancreatography) or ERCP (Endoscopic Retrograde Cholangiopancreatography). This test can demonstrate the presence of two separately draining ducts within the pancreas. Other tests can assist doctors with diagnosis, such as a CT scan and an MRI.

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.

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.

Timo cysts may spontaneously resolve or with pressure directed toward the nose; however, nasolacrimal duct probing may be required to open the obstruction.

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.

The condition is usually self-limiting, and thus not indicated for surgery.

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.

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