Pain and swelling or focal mass at the level of the joint. The pain may be related to a meniscal tear or distension of the knee capsule or both. The mass varies in consistency from soft/fluctuant to hard. Size is variable, and meniscal cysts are known to change in size with knee flexion/extension.

A meniscal cyst is a well-defined cystic lesion located along the peripheral margin of the meniscus, a part of the knee, nearly always associated with horizontal meniscal tears.

The average size of these cysts is 2.0 cm, but excised cysts of more than 5 cm have been reported. The size of the cyst may vary over time and may increase after activity.

These cysts most frequently occur around the dorsum of the wrist and on the fingers. A common site of occurrence is along the extensor carpi radialis brevis, as it passes over the dorsum of the wrist joint. Although most commonly found in the wrist, ganglion cysts also may occur in the foot.

Ganglion cysts are "commonly observed in association with the joints and tendons of the appendicular skeleton, with 88% 'in communication with the multiple small joints of the hand and wrist' and 11% with those of the foot and ankle." They commonly are found near the wrist joint, especially at the scapho-lunate area.

In a 2007 study of patients in Glasgow whose foot lumps were being removed surgically, 39 of 101 cases were ganglion cysts. The study replicated earlier findings that no ganglion cysts were found on the sole or heel of the foot; the authors wrote that "Although lumps in these areas may be ganglia, the surgeon should probably consider other diagnoses in the first instance." The researchers also noted a marked preponderance of occurrence among females (85%) and that 11 of the other cases had been misdiagnosed as ganglion cysts before surgery.

Ganglion cysts are not limited to the hands and feet. They may occur near the knee, commonly near the cruciate ligaments, but also they may occur at the origins of the gastrocnemius tendon and, anteriorly, on Hoffa's infrapatellar fat pad. At the shoulder, they typically occur at the acromioclavicular joint or along the biceps tendon.

From their common origin at a joint or tendon, ganglion cysts may form in a wide range of locations. Rarely, intraosseous ganglion cysts occur, sometimes in combination with a cyst in the overlying soft tissue. Very rare cases of intramuscular ganglion cysts in the gastrocnemius muscle of the calf have been reported. It is possible for a cyst to be displaced considerably from its connection to the joint. In one extreme case, a ganglion cyst was observed to propagate extensively via the conduit of the common peroneal nerve sheath to a location in the thigh; in such cases surgery to the proximal joint to remove the articular connection may remove the need for a riskier, more extensive surgery in the neural tissue of the thigh. The cysts may intrude into the spine, which may cause pain and dysesthesia in distant extremities.

It has been proposed recently that cystic adventitial disease, in which a cyst occurs within the popliteal artery near the knee, may occur by an articular mechanism, with a conduit leading from the joint, similar to the development of ganglion cysts, that spreads within the peroneal nerve.

Cysts that were compressing one or more nerves and causing bone erosions have been reported to occur near the shoulder joint.

Pilonidal cysts are itchy and are often very painful, and typically occur between the ages of 15 and 35. Although usually found near the coccyx, the condition can also affect the navel, armpit or genital region, though these locations are much rarer.

Symptoms include:

- Pain/discomfort or swelling above the anus or near the tailbone that comes and goes

- Opaque yellow (purulent) or bloody discharge from the tailbone area

- Unexpected moisture in the tailbone region

- Discomfort with sitting on the tailbone, doing sit-ups or riding a bike (any activities that roll over the tailbone area)

Some people with a pilonidal cyst will be asymptomatic.

A Baker's cyst, also known as a popliteal cyst, is a benign swelling of the semimembranosus or more rarely some other synovial bursa found behind the knee joint. It is named after the surgeon who first described it, William Morrant Baker (1838–1896). It is not a "true" cyst, as an open communication with the synovial sac is often maintained.

Diagnosis is by examination. A Baker's cyst is easier to see from behind with the patient standing with knees fully extended. It is most easily palpated (felt) with the knee partially flexed. Diagnosis is confirmed by ultrasonography, although if needed and there is no suspicion of a popliteal artery aneurysm then aspiration of synovial fluid from the cyst may be undertaken with care. An MRI image can reveal presence of a Baker's cyst.

An infrequent but potentially life-threatening complication, which may need to be excluded by blood tests and ultrasonography, is a deep vein thrombosis (DVT). Quick assessment of the possibility of DVT may be required where a Baker's cyst has compressed vascular structures, causing leg edema, as this sets up conditions for a DVT to develop.

A burst cyst commonly causes calf pain, swelling and redness that may mimic thrombophlebitis.

A sinus tract, or small channel, may originate from the source of infection and open to the surface of the skin. Material from the cyst may drain through the pilonidal sinus. A pilonidal cyst is usually painful, but with draining, the patient might not feel pain.

Thyroglossal duct cysts most often present with a palpable asymptomatic midline neck mass above the level of the hyoid bone. The mass on the neck moves during swallowing or on protrusion of the tongue because of its attachment to the tongue via the tract of thyroid descent. Some patients will have neck or throat pain, or dysphagia.

The persistent duct or sinus can promote oral secretions, which may cause cysts to become infected. Up to half of thyroglossal cysts are not diagnosed until adult life. The tract can lie dormant for years or even decades, until some kind of stimulus leads to cystic dilation. Infection can sometimes cause the transient appearance of a mass or enlargement of the cyst, at times with periodic recurrences. Spontaneous drainage may also occur. Differential diagnosis are ectopic thyroid, enlarged lymph nodes, dermoid cysts and goiter.

Thyroglossal cyst usually presents as a midline neck lump (in the region of the hyoid bone) that is usually painless, smooth and cystic, though if infected, pain can occur. There may be difficulty breathing, dysphagia (difficulty swallowing), or dyspepsia (discomfort in the upper abdomen), especially if the cyst becomes large.

The most common location for a thyroglossal cyst is midline or slightly off midline, between the isthmus of the thyroid and the hyoid bone or just above the hyoid bone. A thyroglossal cyst can develop anywhere along a thyroglossal duct, though cysts within the tongue or in the floor of the mouth are rare.A thyroglossal cyst will move upwards with protrusion of the tongue.Thyroglossal cysts are associated with an increased incidence of ectopic thyroid tissue. Occasionally, a lingual thyroid can be seen as a flattened strawberry-like lump at the base of the tongue.

An infected thyroglossal duct cyst can occur when it is left untreated for a certain amount of time or simply when a thyroglossal duct cyst hasn't been suspected. The degree of infection can be examined as major rim enhancement has occurred, located inferior to the hyoid bone. Soft tissue swelling occurs, along with airway obstruction and trouble swallowing, due to the rapid enlargement of the cyst.

With infections, there can be rare cases where an expression of fluid is projected into the pharynx causing other problems within the neck.

Most Bartholin's cysts do not cause any symptoms, although some may cause pain during walking, sitting, or sexual intercourse (dyspareunia). They are usually between 1 and 4 cm, and are located just medial to the labia minora. Most Bartholin's cysts only affect the left "or" the right side (unilateral). Small cysts are usually not painful, but very large cysts can cause significant pain.

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 nasopalatine cyst is the most common non-odontogenic cyst of the oral cavity, at an estimated occurrence rate of 73%.

A urachal cyst is a sinus remaining from the allantois during embryogenesis. It is a cyst which occurs in the remnants between the umbilicus and bladder. This is a type of cyst occurring in a persistent portion of the urachus, presenting as an extraperitoneal mass in the umbilical region. It is characterized by abdominal pain, and fever if infected. It may rupture, leading to peritonitis, or it may drain through the umbilicus. Urachal cysts are usually silent clinically until infection, calculi or adenocarcinoma develop.

These cysts are found most often in young adults and are rare in infancy. The usual symptoms are the result of compression by the cyst, e.g., difficulty breathing or swallowing, cough, and chest pain. Malignant degeneration has been reported in these cysts on rare occasions. Chest x-rays show a smooth density just in front of the trachea or main stem bronchi at the carinal level. When the cyst communicates with the tracheobronchial tree, the air-fluid level may be seen within the cyst.

CT scanning is useful in localizing these cysts.

Most branchial cleft cysts present as a smooth, slowly enlarging lateral neck mass that may increase in size after an upper respiratory tract infection. The fistulas, when present, are asymptomatic, but may become infected.

Buccal bifurcation cyst is an inflammatory odontogenic cyst, of the paradental cysts family, that typically appears in the buccal bifurcation region of the mandibular first molars in the second half of the first decade of life. Infected cysts may be associated with pain.

The size of oral mucoceles vary from 1 mm to several centimeters and they usually are slightly transparent with a blue tinge. On palpation, mucoceles may appear fluctuant but can also be firm. Their duration lasts from days to years, and may have recurrent swelling with occasional rupturing of its contents.

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.

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.

Patients with arachnoid cysts may never show symptoms, even in some cases where the cyst is large. Therefore, while the presence of symptoms may provoke further clinical investigation, symptoms independent of further data cannot—and should not—be interpreted as evidence of a cyst's existence, size, location, or potential functional impact on the patient.

Symptoms vary by the size and location of the cyst(s), though small cysts usually have no symptoms and are discovered only incidentally. On the other hand, a number of symptoms may result from large cysts:

- Cranial deformation or macrocephaly (enlargement of the head), particularly in children

- Cysts in the suprasellar region in children have presented as bobbing and nodding of the head called bobble-head doll syndrome.

- Cysts in the left middle cranial fossa have been associated with ADHD in a study on affected children.

- Headaches. A patient experiencing a headache does not necessarily have an arachnoid cyst.

- In a 2002 study involving 78 patients with a migraine or tension-type headache, CT scans showed abnormalities in over a third of the patients, though arachnoid cysts only accounted for 2.6% of patients in this study.

- A study found 18% of patients with intracranial arachnoid cysts had non-specific headaches. The cyst was in the temporal location in 75% of these cases.

- Seizures

- Hydrocephalus (excessive accumulation of cerebrospinal fluid)

- Increased intracranial pressure

- Developmental delay

- Behavioral changes

- Nausea

- Hemiparesis (weakness or paralysis on one side of the body)

- Ataxia (lack of muscle control)

- Musical hallucination

- Pre-senile dementia, a condition often associated with Alzheimer's disease

- In elderly patients (>80 years old) symptoms were similar to chronic subdural hematoma or normal pressure hydrocephalus:

- Dementia

- Urinary incontinence

- Hemiparesis

- Headache

- Seizures

Symptoms are assessed on a case by case basis. Some cysts in the CNS can be asymptomatic (producing or showing no symptoms), depending on their location in the brain or spinal cord. If the cysts develop in critical areas of the central nervous system, they can present one or more of the following symptoms:

- Pressure in the spinal cord or brain

- Rupture of nerves around the cyst

- Weakness in specific parts of the body controlled by the cyst-infected brain region

- Inflammation

- Hydrocephalus

- Brainstem hemorrhage

- Seizures

- Visual disturbances and hearing Loss

- Headache

- Difficulty with balance or walking

In general, symptoms vary depending on the type of cyst and its location within the CNS.

The median palatal cyst is a rare cyst that may occur anywhere along the median palatal raphe. It may produce swelling because of infection and is treated by excision or surgical removal.

Some investigators now believe that this cyst represents a more posterior presentation of a nasopalatine duct cyst, rather than a separate cystic degeneration of epithelial rests at the line of fusion of the palatine shelves.

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.

The most common location to find a mucocele is the inner surface of the lower lip. It can also be found on the inner side of the cheek (known as the buccal mucosa), on the anterior ventral tongue, and the floor of the mouth. When found on the floor of the mouth, the mucocele is referred to as a ranula. They are rarely found on the upper lip. As their name suggests they are basically mucus lined cysts and they can also occur in the Paranasal sinuses most commonly the frontal sinuses, the frontoethmoidal region and also in the maxillary sinus. Sphenoid sinus involvement is extremely rare.

When the lumen of the vermiform appendix gets blocked due to any factor, again a mucocele can form.