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Branchial cyst and fistula: persistent pharyngeal cleft

A branchial (pharyngeal) cyst or fistula (an abnormal opening onto the neck skin) is a leftover of one of the later pharyngeal clefts, grooves on the embryo's outer neck.

Remember

One of the later pharyngeal clefts (the second to fourth) that is not closed over can leave a branchial cyst, a fluid-filled lump at the side of the neck, or a fistula, an opening onto the neck skin; clefts are the outside grooves and pouches the inside pockets.

In the embryo the neck develops from paired ridges called pharyngeal arches. Between the arches, a groove on the outside is called a pharyngeal cleft, while the matching pocket on the inside is called a pouch. Clefts are on the outside and pouches on the inside, and the cleft remnants are the ones that reach the neck skin.

Normally only the first cleft leaves a permanent structure, the ear canal (the external acoustic meatus). The second, third and fourth clefts form temporary pits, and the fast-growing second arch grows over them and closes them off. This closing over is called obliteration. If obliteration is incomplete, a skin-lined remnant (a leftover) can persist.

A branchial cyst is an enclosed, fluid-filled remnant. A branchial fistula is an abnormal opening onto the skin of the neck. A lined tract (a channel between the skin and the deeper neck) that opens onto the skin is called a branchial sinus or fistula. Anomalies of the second arch and cleft account for about 95 per cent of branchial anomalies.

The position of a neck lump is the best clue. A branchial cyst typically presents as a lateral neck lump along the anterior border of the sternocleidomastoid muscle, which lies in the side of the neck. It may be noticed in childhood or not until adulthood, and it can swell when infected. A thyroglossal duct cyst, left behind as the thyroid gland descends from the tongue into the neck, usually lies in the midline. The definitive treatment of a branchial cyst is surgical removal.

Key facts

First cleft
Normally only the first cleft persists, as the ear canal (the external acoustic meatus).
Second to fourth clefts
they form temporary pits that the fast-growing second arch closes over.
Branchial cyst
an enclosed, fluid-filled remnant that typically presents as a lateral neck lump.
Branchial fistula
an abnormal opening onto the skin of the neck, and fistulas tend to present earlier than cysts.
Frequency
anomalies of the second arch and cleft account for about 95 per cent of branchial anomalies.
Site
a branchial cyst typically lies in the lateral neck, along the anterior border of sternocleidomastoid.

Exam traps

  • A lump at the side of the neck does not fit a thyroglossal duct cyst, because a persistent thyroglossal duct usually forms a cyst in the midline of the neck.
  • A pouch remnant is the wrong embryological structure for a branchial cyst, because pouches are the inner pockets between the arches and a branchial cyst comes from the outer clefts.
  • Enlarged lymph nodes (glands) in response to infection are an acquired response, not a congenital remnant, and a branchial cyst itself is present from birth even though it can swell when infected.

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Last updated 7 November 2026. For medical education only, not clinical advice.