Congenital Neck Cysts: Detailed Guide

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

How do congenital neck cysts form?

In the first weeks of development in the womb, the structures of the face, neck and throat take shape from embryonic tissues that fold and fuse together. During this process, some structures travel a long way before settling into place, while some channels and pockets that form temporarily close up and disappear. When this closure is incomplete, the remnant left behind can gradually fill with secretions from the cells lining it and turn into a cyst.

Although the remnant is present from birth, it often goes unnoticed for years. The cyst most often appears as a painless, soft lump; sometimes it is noticed when it swells up after an upper respiratory tract infection, as the secretions inside it increase and the surrounding tissue reacts. This is why congenital cysts may be noticed for the first time not only in childhood but also in young adulthood.

The congenital masses commonly seen in the neck are the thyroglossal duct cyst and branchial cleft anomalies, followed less often by dermoid cysts. There are also other congenital conditions, such as the lymphatic malformations seen in infancy; this article focuses on these three types of cyst.

Thyroglossal duct cyst

The thyroid gland forms at the base of the tongue in the womb and moves down towards its normal place in the lower part of the neck. As it moves down, it leaves behind a thin tract called the thyroglossal duct. The duct normally closes and disappears on its own; if part of it does not close, a thyroglossal duct cyst can develop from this remnant. The thyroglossal duct cyst is the most common congenital mass in the neck.

How is it noticed?

The cyst is most often found in the middle of the front of the neck, at the level of or slightly below the hyoid bone, the small bone just above the larynx; sometimes it may lie a little to one side of the midline. It is soft, round and usually painless. Because the duct remnant is attached to the hyoid bone and the base of the tongue, the cyst usually moves upwards when you swallow and when you stick out your tongue; this is an important clue on examination. The thyroid gland and its nodules also move when you swallow, but they usually do not move when you stick out your tongue; even so, telling them apart relies on examination together with ultrasound (goiter and thyroid diseases).

The cyst is often noticed in childhood, but it can also appear for the first time in adulthood. When it becomes infected, it turns red and painful, and sometimes it may open onto the skin, leaving a hole that leaks fluid.

Assessing the thyroid gland before surgery

Rarely, the lump in the middle of the neck is not a cyst but thyroid tissue that has not fully moved down to its normal place (ectopic thyroid), and in some people this may be the only thyroid tissue in the body. Because removing such tissue could lead to a lack of thyroid hormone, ultrasound is used before surgery to confirm that the thyroid gland is in its normal place and has a normal structure. If considered necessary, thyroid function tests or additional imaging may also be requested.

The Sistrunk operation: why is the central part of the hyoid bone removed?

The hyoid bone develops in this area after the thyroglossal duct has formed. The duct most often passes in front of the hyoid bone, sometimes through or behind it, and may curve below and behind the bone; this is why the remnants of the duct lie in close contact with the hyoid bone. Removing the cyst alone leaves these thin remnants in place, so the chance of the cyst forming again increases markedly.

In the Sistrunk operation, named after the surgeon who described the technique, the cyst, the central part of the hyoid bone and the part of the duct extending towards the base of the tongue are removed in one piece. Studies show that the cyst comes back markedly less often with this method than after removal of the cyst alone; this is why the Sistrunk operation is the standard surgical method for a thyroglossal duct cyst. Removing the central part of the hyoid bone does not usually affect speech or swallowing in the long term.

Branchial cleft cyst, sinus and fistula

In the first weeks of development, ridges called branchial (pharyngeal) arches, which resemble the gills of fish, form in the neck region of the embryo. Between these arches there are clefts on the outside and pouches on the inside. The arches later develop into various structures of the ear, jaw, neck and throat; some of the clefts and pouches between them form structures such as the outer ear canal, the middle ear and the tonsil bed, and the rest normally disappear. A branchial anomaly develops from a remnant that does not disappear. In children, branchial anomalies are the second most common group of congenital neck lesions after the thyroglossal duct cyst.

Depending on the shape of the remnant, three forms can be seen:

• Cyst: a closed, fluid-filled sac that does not open onto the skin or into the throat.
• Sinus: a blind tract that opens at only one end, most often onto the skin of the neck.
• Fistula: a complete channel with one end opening onto the skin of the neck and the other into the throat.

Second branchial cleft anomalies

The great majority of branchial anomalies arise from the second cleft. A second branchial cleft cyst lies at the side of the neck, most often below the angle of the jaw, along the front edge of the sternocleidomastoid muscle. It is usually noticed in late childhood or young adulthood as a painless, soft lump. It may grow during upper respiratory tract infections and then shrink again; sometimes it becomes infected and turns red and painful.

The skin opening of a sinus or fistula, on the other hand, is often noticed from birth: a pinhole-sized opening is seen in the lower part of the neck, along the front edge of the same muscle, and from time to time clear or mucus-like fluid comes out of it. The fistula tract can run upwards through the neck, passing between the blood vessels of the neck, as far as the tonsil area. Sometimes it occurs on both sides. When it occurs on both sides together with an unusual ear shape or hearing loss, these findings may be part of an inherited syndrome (branchio-oto-renal syndrome), so additional tests such as a hearing test and a kidney ultrasound may also be carried out.

Less common types

First branchial cleft anomalies occur around the ear, in front of the ear or just below the angle of the jaw; they may show up as a lump around the ear that keeps becoming infected, or as unexplained discharge from the ear. Because the facial nerve and the salivary gland in front of the ear (the parotid gland) lie close by in this area, surgery is planned so as to protect these structures (salivary gland diseases). Third and fourth pouch anomalies are rare; they may show up as repeated infections around the thyroid gland in the lower part of the neck, most often on the left side. For these types, besides open surgery, endoscopic closure of the tract’s internal opening in the lower part of the throat is also one of the treatment options.

Dermoid cyst

A dermoid cyst forms when cells of the skin and its associated structures become trapped beneath the skin during development. It contains a thick, cheese-like material (keratin) produced by skin cells. In the neck it is most often found in the midline, under the chin; it grows slowly, is painless and feels doughy to the touch. Unlike a thyroglossal cyst, it usually does not move when you stick out your tongue. Treatment is removal of the cyst in one piece; when it has no connection to the hyoid bone, the hyoid bone is left untouched. It is not always possible to tell the two types of cyst apart before surgery; the distinction sometimes becomes clear from the findings at surgery and the pathology examination.

If the cyst becomes infected

Because of the secretions inside them and the connection that some of them have with the mouth or throat, congenital cysts tend to become infected. An infected cyst quickly gets bigger, turns red and becomes painful and tender; there may be a fever. Treatment starts by bringing the infection under control; your doctor decides which medicine to use and how. If the infection progresses and an abscess forms, it may need to be drained with a needle or through a small incision.

During an infection, the tissues are swollen and tend to bleed, which makes removing the cyst more difficult. This is why surgery is planned once the infection has cleared and the tissues have settled. Because a cyst that has been infected once can become infected again, it is advisable to remove the cyst at a suitable time while it is not infected.

Examination and imaging

Assessment starts with questions about when the lump was noticed, whether its size has changed, how it relates to infections, whether it has been infected or leaked fluid before, and any previous operations. On examination, the location, consistency and mobility 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; in adults, the back of the nose, the throat and the larynx are also looked at endoscopically with a thin camera.

• Ultrasound: this is the first-choice method in children and for lumps in the middle of the neck. It involves no radiation and can easily be done in children too. It shows the structure and size of the cyst and its relationship to the hyoid bone and the surrounding tissues; with a thyroglossal cyst, it confirms that the thyroid gland is in its normal place.
• MRI or CT scan: these may be needed for anomalies that are infected, extend deep, have come back or lie around the ear, to see the relationship of the cyst to nearby structures in detail. They are also often used to assess cystic lumps at the side of the neck in adults.
• Fine-needle aspiration biopsy: when the diagnosis is not clear, especially in adults, a sample of fluid and cells can be taken from the cyst with a thin needle under ultrasound guidance.

A cystic lump at the side of the neck in adults

Branchial cleft cysts are also seen in young adults. However, a cystic lump noticed for the first time at the side of the neck in adulthood is not always a branchial cyst: some lymph nodes can also take on a fluid-filled appearance during illness and mimic a branchial cyst. It is not always possible to make this distinction by feeling the lump alone.

This is why, in adults, cystic lumps at the side of the neck are assessed step by step until the diagnosis is clear: the throat, the back of the nose and the larynx are examined endoscopically, an MRI or CT scan is often done in addition to ultrasound, and a fine-needle aspiration biopsy under ultrasound guidance is taken when needed. The clinical practice guideline on evaluating neck masses in adults also notes that in a lump that has been present for more than two weeks and cannot be explained by an infection, for example, a cystic appearance alone does not show that it is a branchial cyst; it recommends continuing the assessment until the diagnosis is clear. This step-by-step assessment does not mean that the lump is a serious condition; it ensures that the lump is correctly identified and that treatment is planned accordingly (lymph nodes in the neck).

Surgery and recovery

Congenital neck cysts are treated with surgery. 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. The aim is to remove the cyst completely, together with any duct or fistula tract connected to it, without leaving any remnant behind.

• For a thyroglossal duct cyst: in the Sistrunk operation, the cyst, the central part of the hyoid bone and the duct extending to the base of the tongue are removed together.
• For a branchial cleft cyst or fistula: the cyst and its tract are removed, with care taken to protect the surrounding blood vessels and nerves. For long fistula tracts, two small incisions may be needed, one around the skin opening and one higher up.
• For a dermoid cyst: the cyst is removed in one piece without tearing its wall.

A thin drain may be placed to prevent blood and fluid from collecting at the operation site; the drain is usually removed within a short time. The hospital stay is usually short. In the first days there may be mild pain and tightness in the neck, and after thyroglossal cyst surgery there may be pain on swallowing. Uncommon problems include wound infection, a collection of blood or fluid under the wound and the cyst coming back. In branchial anomaly surgery, the nerves that pass through the operation area may rarely be affected temporarily (for example, slightly reduced movement at the corner of the mouth); these structures are protected during the operation. The tissue removed is sent to the pathology laboratory; this examination confirms the diagnosis. Very rarely, a tumour arising from thyroid tissue may be found in the wall of a thyroglossal cyst; in such a case, the next steps are planned according to the pathology result. Advice on wound care, bathing and returning to daily activities is given separately after surgery.

Recurrence

If a small remnant of the cyst wall or of the duct or tract is left behind, the cyst can form again. With a thyroglossal cyst, the main factor that determines the chance of recurrence is the type of operation performed; after the Sistrunk operation, recurrence is markedly less common than after removal of the cyst alone. Wound infection after surgery has also been linked with recurrence. With branchial anomalies, it is important to remove the fistula tract completely. A recurrent cyst is assessed with ultrasound and, if needed, MRI; treatment is usually further surgery, which requires more careful planning because it is carried out in an area that has already been operated on.

Congenital neck cysts in children

Thyroglossal duct cysts and branchial anomalies are often noticed in childhood. There is no specific age limit for surgery; the operation is planned at a suitable time after diagnosis, while the cyst is not infected. Because the cyst can become infected over time, and infection can make the surrounding tissues stick together (adhesions) and so make surgery more difficult, waiting for a long time is generally not recommended. In very young children, the timing is decided taking into account the child’s general health and anaesthetic considerations. The process before and after surgery, and when the child can go back to school or nursery, are discussed separately with the family.

Frequently asked questions

Will a congenital neck cyst go away with medicine? No. Medicines are used only to bring the infection under control when the cyst becomes infected. Once the infection has cleared, the lump may shrink; however, because the wall of the cyst and the remnant of the duct or tract stay in place, the cyst does not disappear and may swell up again. Draining the fluid with a needle also reduces the swelling only temporarily. Treatment is surgical.

My child has a thyroglossal or branchial cyst; when should the operation be done? There is no specific age limit. If the cyst is not infected, the operation is planned at a suitable time after diagnosis. If the cyst is infected, the infection is treated first and the operation is done once the infection has cleared. The timing is decided together with the family, according to the child’s age, general health and the features of the cyst.

Will there be a scar after surgery? The incision is placed in one of the natural skin creases of the neck so that the scar is less noticeable. The scar may be more visible in the first months and fades over time; its final appearance also depends on how the person’s skin heals. During this time, protecting the wound from the sun and following the wound care advice you are given helps. With cysts that have previously become infected and opened onto the skin, the tissue around the skin opening may also need to be removed.

Can the cyst come back after surgery? Recurrence is possible but not common. If a small remnant of the cyst or of its duct or tract is left behind, the cyst can form again. This chance is markedly reduced by the Sistrunk operation for a thyroglossal cyst and by complete removal of the tract for branchial anomalies. A cyst that comes back can also be treated with further surgery.

The cyst has shrunk on its own; is surgery still needed? Congenital cysts can grow with infections and shrink again when they settle. Shrinking does not mean that the cyst has gone; as long as the remnant remains, it can swell up or become infected again. This is why, once a cyst has been diagnosed, a settled phase is usually a suitable time for surgery. The decision is made together, based on the examination and ultrasound findings.

Does removing part of the hyoid bone cause problems? In the Sistrunk operation, only a small section from the central part of the hyoid bone is removed. This does not usually affect speech, swallowing or the appearance of the neck in the long term. In the first days there may be pain on swallowing and a feeling of tightness in the throat; these complaints ease as healing progresses.

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