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Embryology · Head and neck: pharyngeal arches

Pharyngeal clefts and membranes: external ear and cervical sinus !

  • Embryonic structure

Clefts are outer grooves between the arches. Only the first one stays, as the ear canal. The others close over.

Updated 2026-11-01

See it in 3D: Ear canal · Eardrum · Auricle · Sternocleidomastoid

What it is

Pharyngeal clefts are ectodermal grooves between the arches, and pharyngeal membranes are the thin sheets that separate them from the pouches. Only the first cleft persists, as the external acoustic meatus, and the first membrane, as the tympanic membrane. Clefts 2 to 4 end up inside the cervical sinus, which should disappear; its leftovers are the source of branchial cysts and fistulas.

Key facts

  • The tympanic membrane is the one structure here with input from all three germ layers.
  • Branchial cysts lie along the anterior border of sternocleidomastoid, following the path of the cervical sinus.
  • Preauricular pits relate to the auricular hillocks, not to a cleft.

Structure

  • Cleft: an outer groove lined by ectoderm.
  • Membrane: cleft ectoderm, pouch endoderm and a little mesenchyme between them.
  • Cervical sinus: an ectodermal cavity left when the 2nd arch covers clefts 2, 3 and 4.

What it becomes

  • 1st cleft (dorsal part): external acoustic meatus.
  • 1st membrane: tympanic membrane, with its three layers (ectoderm, mesenchyme and endoderm).
  • Clefts 2 to 4: form the cervical sinus, which normally disappears.
  • The auricle does not come from the cleft but from six hillocks on arches 1 and 2 around it.

Step by step

  1. Week 5: four clefts are visible on each side of the neck.
  2. The dorsal part of the 1st cleft sinks into the mesenchyme and forms the external acoustic meatus.
  3. The 2nd arch grows down and joins the epicardial ridge of the lower neck.
  4. Clefts 2 to 4 lose contact with the outside and form the cervical sinus.
  5. The cervical sinus is obliterated; if not, it leaves a cyst, sinus or fistula.

Clinical notes

  • External auditory canal atresia: failure of the 1st cleft; conductive hearing loss, often with microtia.
  • Cervical sinus remnants: lateral neck cyst, which often shows up in childhood or young adulthood after a respiratory infection.
  • First-cleft anomalies: near the ear or the angle of the jaw, close to the facial nerve and parotid.

Test yourself

Think of the answer, then tap the question to see it.

What does the first pharyngeal cleft form?

The external acoustic meatus.

Which layers form the tympanic membrane?

Ectoderm of the first cleft, endoderm of the first pouch and mesenchyme between them.

What is the cervical sinus, and what happens if it persists?

The cavity left by clefts 2 to 4 under the second arch; if it is not obliterated it gives branchial cysts, sinuses or fistulas.

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See it in 3D

The structures of Durgical's 3D anatomy where it is found.

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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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