Embryology · Head and neck: pharyngeal arches
Branchial cleft cysts, sinuses and fistulas !
- Malformation
A lump or a small opening on the side of the neck, in front of the sternocleidomastoid muscle. It is left over from the grooves of the embryo's neck.
Updated 2026-11-01
See it in 3D: Sternocleidomastoid · Internal carotid artery · External carotid artery · Glossopharyngeal nerve (IX) · Hypoglossal nerve (XII) · Palatine tonsils · Parotid gland · Facial nerve (VII) · Ear canal · Thyroid gland
What it is
Branchial anomalies are leftovers of the clefts, pouches or cervical sinus that did not disappear. They may be a cyst (no opening), a sinus (one opening) or a fistula (two, on the skin and in the pharynx). Most come from the second cleft and lie along the anterior border of sternocleidomastoid, on the side of the neck, unlike the thyroglossal cyst.
Key facts
- The second cleft accounts for most branchial anomalies.
- About 10% are bilateral.
- Definitive treatment is complete excision of the cyst and its tract, away from an acute infection.
- Branchio-oto-renal syndrome (EYA1): branchial cysts or fistulas with hearing loss and kidney anomalies.
Embryological cause
- Week 5: the 2nd arch grows down, covers clefts 2 to 4 and forms the cervical sinus, which should be obliterated.
- If the 2nd arch does not fully cover them or the sinus is not obliterated, an epithelium-lined cyst, sinus or fistula remains.
- Second-cleft fistula: runs from the skin at the front of sternocleidomastoid to the tonsillar fossa, between the internal and external carotids, superficial to IX and XII.
- First-cleft anomalies: near the ear or the angle of the jaw, related to the parotid and facial nerve.
- Third and fourth anomalies: rare, linked to the piriform sinus; the fourth is more often left-sided.
How it presents
- Soft, painless lateral neck mass below the angle of the jaw, in front of sternocleidomastoid.
- Usually noticed in late childhood or young adulthood, when it grows or becomes infected after an upper respiratory infection.
- Sinus or fistula: a pinpoint skin opening in the neck draining mucus or pus.
- First cleft: mass or drainage near the ear, ear canal or angle of the jaw.
- Fourth pouch or cleft: neck abscesses or recurrent left-sided suppurative thyroiditis.
- In an adult, a new cystic lateral neck mass must be checked for a nodal metastasis of squamous cell carcinoma.
Diagnosis
- Ultrasound: confirms a cystic lesion without radiation.
- Contrast CT or MRI to show extent and relation to vessels and nerves.
- Fistulogram to trace a sinus or fistula tract.
- Fine-needle aspiration when in doubt, especially in adults.
Test yourself
Think of the answer, then tap the question to see it.
Which cleft do most branchial cysts come from?
The second pharyngeal cleft.
Between which arteries does a second-cleft fistula pass, and where does it open inside?
Between the internal and external carotid arteries; it opens into the tonsillar fossa.
Which difference in position helps tell a branchial cyst from a thyroglossal cyst?
The branchial cyst is lateral, in front of sternocleidomastoid; the thyroglossal cyst is midline and tied to the hyoid.
What must be ruled out with a new lateral neck cyst in an adult?
A cystic nodal metastasis of squamous cell carcinoma, for example from the oropharynx.
See it in 3D
The structures of Durgical's 3D anatomy where it is found.
- Sternocleidomastoid
- Internal carotid artery
- External carotid artery
- Glossopharyngeal nerve (IX)
- Hypoglossal nerve (XII)
- Palatine tonsils
- Parotid gland
- Facial nerve (VII)
- Ear canal
- Thyroid gland
Related
- Pharyngeal clefts and membranes: external ear and cervical sinus
- Pharyngeal pouches: tonsil, thymus, parathyroids and C cells
- Second pharyngeal arch (hyoid arch) and the facial nerve
- Thyroglossal duct cyst and ectopic thyroid
- Congenital hearing loss, microtia and preauricular pits
Related conditions
- Deep neck infection and Ludwig angina
- Cervical lymphadenopathy
- Head and neck squamous cell carcinoma (oral cavity and oropharynx, HPV)
- Thyroiditis (subacute, painless and postpartum)
Educational content on embryonic development; not a guide to prenatal diagnosis or to medicines in pregnancy and no substitute for a health professional's advice. No doses are given.
Sources: Branchial Cleft Anomalies - StatPearls - NCBI Bookshelf (StatPearls Publishing (NCBI Bookshelf), 2025); Embryology, Pharyngeal Pouch - StatPearls - NCBI Bookshelf (StatPearls Publishing (NCBI Bookshelf), 2023); Langman's Medical Embryology, 13th ed., ch. 17: Head and Neck (Wolters Kluwer, 2015).
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Representative model, for educational purposes only.