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.

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.

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.

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.

A neurosurgeon may open a portion of the body and insert a shunt into cerebral spinal fluid (CSF) filled cysts to allow drainage into CSF pathways. The fluid from the cyst is then drained into the abdomen, the body reabsorbs the fluid (reabsorption of fluid does not cause any harm). This type of surgical treatment is often performed to relieve pressure on the brain from a cyst within the cerebral cortex.

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.

The aneurysmal bone cyst is a neoplastic cyst, more specifically, an aggressive lesion with radiographic cystic appearance.

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.

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:

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.

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.

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

Diagnosis is principally by MRI. Frequently, arachnoid cysts are incidental findings on MRI scans performed for other clinical reasons. In practice, diagnosis of symptomatic arachnoid cysts requires symptoms to be present, and many with the disorder never develop symptoms.

Additional clinical assessment tools that can be useful in evaluating a patient with arachnoid cysts include the mini-mental state examination (MMSE), a brief questionnaire-based test used to assess cognition.

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.

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.

This disease is often discovered during surgery for other conditions, e.g., hernia repair, following which an experienced pathologist can confirm the diagnosis. Advanced stages may present as tumors palpable on the abdomen or distention of the belly ("jelly belly" is sometimes used as a slang term for the condition). Due to the rarity of this disease, it is important to obtain an accurate diagnosis so that appropriate treatment may be obtained from a surgical oncologist who specializes in appendix cancer. Diagnostic tests may include CT scans, examination of tissue samples obtained through laparoscopy, and the evaluation of tumor markers. In most cases a colonoscopy is unsuitable as a diagnostic tool because in most cases appendix cancer invades the abdominal cavity but not the colon (however, spread inside the colon is occasionally reported). PET scans may be used to evaluate high-grade mucinous adenocarcinoma, but this test is not reliable for detecting low-grade tumors because those do not take up the dye which shows up on scans. New MRI procedures are being developed for disease monitoring, but standard MRIs are not typically used as a diagnostic tool. Diagnosis is confirmed through pathology.

a nuclear imaging method to evaluate any degenerative and/or arthritic changes in the joints; to detect bone diseases and tumors; to determine the cause of bone pain or inflammation. This test is to rule out other cysts (which are quite unusual)

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.

Various management options exist depending on the severity of symptoms and their effect on the patient. The main management options are: observation, craniotomy for microsurgical resection, neuroendoscopic removal, stereotactic drainage, and cerebrospinal fluid diversion with bilateral ventriculoperitoneal shunting placement.

CT scans use x-rays and computer technology to produce accurate axial, coronal, and sagittal images. CT scans are more detailed than x-rays because they can create images that show fat, muscles, organs, and bones.