Congenital Neck Cysts (Thyroglossal and Branchial Cysts)

Author: Op. Dr. Javidan Asafov · ENT / Otolaryngology Specialist · Last medical review: 22.10.2026

What is it?

The neck takes shape in the first weeks of development in the womb, as many structures move into place and join together. During this process, a small channel or pocket that would normally close and disappear sometimes does not go away completely, or skin cells may become trapped beneath the skin. Over time, this remnant can fill with fluid or secretions and turn into a cyst. This is why these cysts are called congenital neck cysts.

The remnant is present from birth, but the cyst is often not apparent at birth and is usually noticed in childhood or young adulthood. It most often appears as a painless lump; sometimes it first shows itself by swelling up after a cold or a throat infection. Congenital neck cysts are benign. Because they tend to become infected and do not go away with medicine, they are usually treated with surgery.

Types

• Thyroglossal duct cyst: This is the most common congenital cyst in the neck. The thyroid gland forms at the base of the tongue in the womb, and as it moves down to its place in the lower part of the neck, it leaves a thin duct behind it. If this duct does not close, a cyst forms in the middle of the front of the neck, most often at the level of or just below the hyoid bone, the small bone above the larynx. Because the cyst is attached to the hyoid bone and the base of the tongue by the duct remnant, it usually moves upwards when you swallow and when you stick out your tongue.
• Branchial cleft cyst, sinus and fistula: These are remnants of the clefts and pouches between the branchial (pharyngeal) arches, which play a part in the development of the face and neck. They are most often found at the side of the neck, along the front edge of the large neck muscle that runs from behind the ear towards the breastbone (the sternocleidomastoid muscle). Remnants of the second branchial cleft are the most common. If the remnant is a closed sac, it is called a cyst; if it is a blind tract that opens at only one end (most often onto the skin), it is called a sinus; and if it opens both onto the skin and into the throat, it is called a fistula.
• Dermoid cyst: A slow-growing cyst containing skin cells, usually found under the chin, in the midline. Unlike a thyroglossal cyst, it usually does not shift with movements of the tongue.

Symptoms

Common findings are:

• A painless lump: a soft, round and usually painless lump in the middle or at the side of the neck.
• Growing with infections: the lump gets bigger during a cold or throat infection and shrinks once the infection has passed.
• Infection: when the cyst becomes infected, there is redness, pain, tenderness and sometimes a fever; an infected cyst may open onto the skin by itself.
• A small hole that leaks fluid: with a branchial sinus or fistula, clear or thicker fluid comes out from time to time through a pinhole-sized opening in the skin of the neck, which is usually present from birth.
• Movement on swallowing: a thyroglossal duct cyst usually moves upwards when you swallow and when you stick out your tongue.
• A feeling of fullness: large cysts can cause a feeling of fullness in the neck or a slight catching sensation when swallowing.

Examination and diagnosis

Assessment starts with questions about how long the lump has been there, whether its size has changed, whether it has been infected before and whether it has leaked fluid. On examination, the location and consistency of the cyst are assessed, along with whether it moves when you swallow and when you move your tongue; the mouth and throat are examined and, if needed, the back of the nose and the larynx are looked at endoscopically with a thin camera.

In children and for lumps in the middle of the neck, the first choice of imaging is an ultrasound scan of the neck. Ultrasound shows the structure of the cyst and its relationship to the surrounding tissues; with a thyroglossal cyst, ultrasound is also used before surgery to confirm that the thyroid gland is in its normal place (goiter and thyroid diseases). If needed, an MRI or CT scan may be requested; in adults, these scans are used more often, in addition to ultrasound, for cystic lumps at the side of the neck. In adults, a newly noticed cystic lump at the side of the neck is carefully assessed to distinguish it from a lymph node that can look fluid-filled; for this, a fine-needle aspiration biopsy under ultrasound guidance is carried out if needed (lymph nodes in the neck).

Treatment

Congenital cysts do not go away with medicine. Medicines are used only to bring the infection under control when the cyst becomes infected; your doctor decides which medicine to use and how. Draining the fluid inside the cyst with a needle also reduces the swelling only temporarily; because the wall of the cyst stays in place, the cyst usually fills up again.

• Infection first: if the cyst is infected, the infection is treated first; if an abscess has formed, it may need to be drained with a needle or through a small incision. Surgery is planned once the infection has cleared and the tissues have settled.
• The Sistrunk operation for a thyroglossal duct cyst: the cyst is removed together with the central part of the hyoid bone and the duct remnant extending towards the base of the tongue. Because the duct runs very close to the hyoid bone, most often in front of it and sometimes through or behind it, removing the cyst alone increases the chance of the cyst forming again; removing the central part of the hyoid bone as well markedly reduces this chance.
• For branchial cleft anomalies: the cyst and, if present, the whole sinus or fistula tract are removed. For long fistula tracts, two small incisions in the neck may be needed.
• For a dermoid cyst: the cyst is separated from the surrounding tissues and removed in one piece.

The operation is performed under general anaesthesia. The incision is placed in one of the natural skin creases of the neck so that the scar is less noticeable. A thin drain may be placed to remove any blood and fluid that collects at the operation site. The hospital stay is usually short. The tissue removed is sent to the pathology laboratory for examination.

What should you keep in mind in daily life?

• Do not squeeze the cyst: squeezing the lump or trying to drain it yourself can lead to infection.
• Keep track of changes: noting when the lump gets bigger or smaller and, if possible, taking photos is helpful at the examination.
• Keep a leaking opening clean: gently clean the opening of the sinus or fistula with soap and water; do not put anything into the opening and do not squeeze it.
• Be watchful during infections: if the lump gets bigger, turns red or becomes painful during a cold or throat infection, do not put off an examination.
• After surgery: follow the advice you are given on wound care, bathing and returning to daily activities; protecting the wound area from the sun in the first months helps the scar fade better.

When to see a specialist

It is advisable to see an ENT specialist if you notice a lump in the neck that lasts longer than two weeks or keeps swelling up and going down, a small hole in the skin of the neck that leaks fluid, or a lump that moves when you swallow. Do not put off an examination if the lump becomes red and painful, grows quickly, makes swallowing difficult or is accompanied by a fever. A lump noticed for the first time at the side of the neck in adulthood should also be assessed, rather than waiting for it to shrink on its own. Congenital neck cysts are benign; an accurate diagnosis and surgery carried out at a suitable time help prevent repeated infections.

This article is for general information; please consult your physician for diagnosis and treatment.