Branchial cleft anomalies

Branchial cleft anomalies comprise of a spectrum of congenital defects that occur in the head and neck.


The anomalies result from branchial apparatus (six arches; five clefts), which are the embryologic precursors of the ear and the muscles, blood vessels, bones, cartilage, and mucosal lining of the face, neck, and pharynx 1.

During the 3rd to 5th week of embryonic development, the second arch grows caudally and covers the third, fourth and sixth arches. When it fuses to the skin caudal to these arches, the cervical sinus is formed. Eventually, the edges of cervical sinus fuse and the ectoderm within the tube disappears 9. Persistence of branchial cleft or pouch results in a cervical anomaly located along the anterior border of the sternocleidomastoid muscle from the tragus of the ear to the clavicle 10.

The range of anomalies can include:

  • cyst: no internal or external communication
  • fistula: communicates both internally and externally
  • sinus: incomplete tract

Cysts are the most common, outnumbering fistulas and sinuses ~2:1 6. Among fistulae and sinuses, the order prevalence is thought to be: external draining sinus > complete fistula > internal draining sinus 6; although some anomalies can occur in combination.

The full list of branchial anomalies includes:

The 3rd and 4th branchial arches tend to be very close and therefore the distinction between these two cleft anomalies can be difficult on imaging 7-8.

Differential diagnosis

  • Paramedian thyroglossal duct cysts (usually branchial cleft cysts are well away from the midline)
  • thyroid nodules and cysts
  • necrotic lymph node metastases (e.g. from squamous cell and papillary thyroid carcinomas)
  • infectious adenitis (e.g. tuberculosis)
  • vascular lesion on non-enhanced CT images (e.g. mycotic aneurysm)
  • lymphatic malformations
  • neurogenic tumors with cystic degeneration (e.g. schwannomas)
  • cervical dermoid cysts

Article information

rID: 10935
System: Head & Neck
Synonyms or Alternate Spellings:
  • Branchial cleft cysts
  • Branchial cleft cysts - general
  • Branchial cleft anomaly

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Cases and figures

  • Figure 1: pharyngeal arches (diagram)
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  • Case 1
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  • Case 2
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  • Case 3: 2nd branchial cleft cyst
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  • Case 4: probable 3rd branchial cleft cyst
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  • Case 5: 4th branchial cleft cyst
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