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.

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.

A cyst is a closed sac, having a distinct membrane and division compared with the nearby tissue. Hence, it is a cluster of cells that has grouped together to form a sac (not unlike the manner in which water molecules group together, forming a bubble); however, the distinguishing aspect of a cyst is that the cells forming the "shell" of such a sac are distinctly abnormal (in both appearance and behaviour) when compared with all surrounding cells for that given location. It may contain air, fluids, or semi-solid material. A collection of pus is called an abscess, not a cyst. Once formed, sometimes a cyst may resolve on its own. When a cyst fails to resolve, it may need to be removed surgically, but that would depend upon its type and location.

Cancer-related cysts are formed as a defense mechanism for the body, following the development of mutations that lead to an uncontrolled cellular division. Once that mutation has occurred, the affected cells divide incessantly (and become known as cancerous), forming a tumour. The body encapsulates those cells to try to prevent them from continuing their division and to try to contain the tumour, which becomes known as a cyst. That said, the cancerous cells still may mutate further and gain the ability to form their own blood vessels, from which they received nourishment before being contained. Once that happens, the capsule becomes useless and the tumour may advance from benign to a cancer.

Some cysts are neoplastic and thus, are called cystic tumors; many types are not neoplastic. Some are dysplastic or metaplastic. Pseudocysts are similar to cysts (having a sac filled with fluid), but lack an epithelial lining.

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.

Signs and symptoms of pancreatic pseudocyst include abdominal discomfort and indigestion.

A mesenteric cyst () is a cyst in the mesenterium, and is one of the rarest abdominal tumors, with approximately 822 cases reported since 1507. The incidence is between 1 per 100,000 to 1 per 250,000 hospital admissions.

Tillaux's triad named after the french surgeon Paul Jules Tillaux can be seen in cases of mesenteric cyst. It consists of the following signs:

- a fluctuating swelling near the umbilicus,

- freely mobile in the direction perpendicular to the attachment of mesentry,

- with a zone of resonance around the swelling.

Complication of pancreatic pseudocyst include infection, hemorrhage, obstruction and rupture. For obstruction, it can cause compression in the GI tract from the stomach to colon, compression in urinary system, biliary system, and arteriovenous system.

A central nervous system cyst is a type of cyst that presents and affects part of the central nervous system (CNS). They are usually benign and filled with either cerebrospinal fluid, blood, or tumor cells. CNS cysts are classified into two categories: cysts that originate from non-central nervous system tissue, migrate to, and form on a portion of the CNS, and cysts that originate within central nervous system tissue itself. Within these two categories, there are many types of CNS cysts that have been identified from previous studies.

The majority of people with a Meckel's diverticulum are asymptomatic. An asymptomatic Meckel's diverticulum is called a "silent" Meckel's diverticulum. If symptoms do occur, they typically appear before the age of two years.

The most common presenting symptom is painless rectal bleeding such as melaena-like black offensive stools, followed by intestinal obstruction, volvulus and intussusception. Occasionally, Meckel's diverticulitis may present with all the features of acute appendicitis. Also, severe pain in the epigastric region is experienced by the patient along with bloating in the epigastric and umbilical regions. At times, the symptoms are so painful that they may cause sleepless nights with acute pain felt in the foregut region, specifically in the epigastric and umbilical regions.

In some cases, bleeding occurs without warning and may stop spontaneously. The symptoms can be extremely painful, often mistaken as just stomach pain resulting from not eating or constipation.

Rarely, a Meckel's diverticulum containing ectopic pancreatic tissue can present with abdominal pain and increased serum amylase levels, mimicking acute pancreatitis.

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.

Anomalies between the diverticulum and umbilicus may include the presence of fibrous cord, cyst, fistula or sinus, leading to:

- Infection or excoriation of periumbilical skin, resulting in a discharging sinus

- Recurrent infection and healing of sinus

- Abscess formation in the abdominal wall

- Fibrous cord increases the risk of volvulus formation and internal herniation

Dermoid cysts can appear in young children, often near the lateral aspect of the eyebrow (right part of the right eyebrow or left part of the left eyebrow). Depending on the perceived amount of risk, these are sometimes excised or simply kept under observation.

An inflammatory reaction can occur if a dermoid cyst is disrupted, and the cyst can recur if it is not completely excised. Sometimes complete excision is not practical if the cyst is in a dumbbell configuration, whereby it extends through a suture line in the skull.

If dermoid cysts appear on the medial aspect, the possibility of an encephalocele becomes greater and should be considered among the differential diagnoses.

Dermoid cysts develop during pregnancy. They occur when skin cells and things like hair, sweat glands, oil glands or fatty tissue get trapped in the skin as a baby grows in the womb.Dermoid cysts are present at birth (congenital) and are common. It can be months or years before a dermoid cyst is noticed on a child because the cysts grow slowly.

Dermoid cyst symptoms are minor and the cysts are usually painless. They are not harmful to a child’s health. If they become infected, the infection must be treated and the cyst should be removed. It is easier to remove cysts and prevent scars if the cyst is removed before it gets infected.

Due to its classification, a dermoid cyst can occur wherever a teratoma can occur.

Patients (often infants) present acutely with midgut volvulus, manifested by bilious vomiting, crampy abdominal pain, abdominal distention, and the passage of blood and mucus in their stools. Patients with chronic, uncorrected malrotation can have recurrent abdominal pain and vomiting.

Malrotation can also be asymptomatic.

The scalp, ears, back, face, and upper arm, are common sites of sebaceous cysts, though they may occur anywhere on the body except the palms of the hands and soles of the feet. In males a common place for them to develop is the scrotum and chest. They are more common in hairier areas, where in cases of long duration they could result in hair loss on the skin surface immediately above the cyst. They are smooth to the touch, vary in size, and are generally round in shape.

They are generally mobile masses that can consist of:

- Fibrous tissues and fluids,

- A fatty (keratinous) substance that resembles cottage cheese, in which case the cyst may be called "keratin cyst". This material has a characteristic "cheesy" or foot odor smell,

- A somewhat viscous, serosanguineous fluid (containing purulent and bloody material).

The nature of the contents of a sebaceous cyst, and of its surrounding capsule, differs depending on whether the cyst has ever been infected.

With surgery, a cyst can usually be excised in its entirety. Poor surgical technique, or previous infection leading to scarring and tethering of the cyst to the surrounding tissue, may lead to rupture during excision and removal. A completely removed cyst will not recur, though if the patient has a predisposition to cyst formation, further cysts may develop in the same general area.

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

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.

A colloid cyst is a tumor containing gelatinous material in the brain. It is almost always found just posterior to the foramen of Monro in the anterior aspect of the third ventricle, originating from the roof of the ventricle. Because of its location, it can cause obstructive hydrocephalus and increased intracranial pressure. Colloid cysts represent 0.5–1% of intracranial tumors.

Symptoms can include headache, vertigo, memory deficits, diplopia, behavioral disturbances and in extreme cases, sudden death. Intermittency of symptoms is characteristic of this lesion. Untreated pressure caused by these cysts can result in brain herniation. Colloid cyst symptoms have been associated with 4 variables: cyst size, cyst imaging characteristics, ventricular size, and patient age. The developmental origin is unclear, though they may be of endodermal origin, which would explain the mucin-producing, ciliated cell type. These cysts can be surgically resected, and opinion is divided about the advisability of this.

Patients with third ventricular colloid cysts become symptomatic when the tumor enlarges rapidly, causing CSF obstruction, ventriculomegaly, and increased intracranial pressure. Some cysts enlarge more gradually, however, allowing the patient to accommodate the enlarging mass without disruption of CSF flow, and the patient remains asymptomatic. In these cases, if the cyst stops growing, the patient can maintain a steady state between CSF production and absorption and may not require neurosurgical intervention.

Cysts rarely cause any symptoms, unless they become secondarily infected. The signs depend mostly upon the size and location of the cyst. If the cyst has not expanded beyond the normal anatomical boundaries of the bone, then there will be no palpable lump outside or inside the mouth. The vast majority of cysts expand slowly, and the surrounding bone has time to increase its density around the lesion, which is the body's attempt to isolate the lesion. Cysts that have expanded beyond the normal anatomic boundaries of a bone are still often covered with a thin layer of new bone. At this stage, there may be a sign termed "eggshell cracking", where the thinned cortical plate cracks when pressure is applied. A lump may be felt, which may feel hard if there is still bone covering the cyst, or fluctuant if the cyst has eroded through the bone surrounding it. A cyst may become acutely infected, and discharge into the oral cavity via a sinus. Adjacent teeth may be loosened, tilted or even moved bodily. Rarely, roots of teeth are resorbed, depending upon the type of cyst. The inferior alveolar nerve runs through the mandible and supplies sensation to the lower lip and chin. As most cysts expand slowly, there will be no altered sensation (anesthesia or paraesthesia), since the inferior alveolar canal is harmlessly enveloped or displaced over time. More aggressive cysts, or acute infection of any cyst may cause altered sensation.

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.

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.

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 epidermoid cyst may have no symptoms, or it may hurt when touched. It can release pus. It is very common for women on the major or minor labia. In contrast to pilar cysts, epidermoid cysts are usually present on parts of the body with relatively little hair.

Occasionally, an epidermoid cyst will present with Trigeminal neuralgia.

Although they are not malignant, there are rare cases of malignant tumors arising from an epidermoid cyst.