Branchial Cleft Malformations

Branchial Cleft Malformations is a topic covered in the Select 5-Minute Pediatrics Topics.

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  • Phylogenetically, the branchial apparatus represents the “gills” seen in fish and amphibians.
  • The fetal branchial apparatus is a foregut derivative and develops in the 2nd fetal week.
  • Five paired pharyngeal arches are separated by four endodermal pouches internally and four ectodermal clefts externally.
  • Overgrowth of the second through fourth cleft creates the cervical sinus and occurs during weeks 4 and 5.
  • Persistence of the cervical sinus produces a spectrum of cysts, sinus tracts, and fistulae.
  • Classification
    • First branchial cleft anomalies
      • Site: anywhere from external auditory canal to angle of mandible, usually superior to or within parotid
      • Fistula tract: external auditory canal
    • Second branchial cleft anomalies
      • Site: ventral to anterior border of sternocleidomastoid muscle, lateral to carotid sheath, and dorsal to submandibular gland
      • Fistula tract: palatine tonsil
    • Third branchial cleft anomalies
      • Site: posterior triangle in middle to lower left side of the neck near level of upper thyroid lobe
      • Fistula: upper lateral piriform sinus wall to lower lateral neck posterior to sternocleidomastoid muscle
    • Fourth branchial cleft anomalies
      • Site: close association to thyroid gland associated with clinical thyroiditis if cyst infected
      • Fistula: apex of piriform sinus to base of neck anterior to sternocleidomastoid muscle


  • Overwhelming majority of cysts in newborns and infants are developmental, whereas in children and adults, they are inflammatory or neoplastic.
  • Branchial cleft cysts are the most common congenital neck lesion. Although congenital, usually present in older children and adults.
  • Branchial fistula and sinuses are common in children but cysts are more commonly seen in adults.
  • Midline malformations are most often thyroglossal duct cysts or dermoids.
  • Cysts occurring in the laterocervical region are usually branchial cleft malformations; the most common of these are derivatives of the second cleft, followed by those of the first cleft, of the fourth pouch and thymic cysts.
  • Third and fourth branchial cleft anomalies are rare, with most presenting as sinus tracts rather than cysts.
  • Suspect congenital anomaly in the clinical setting of recurrent infection.

Risk Factors


Familial history of branchial defects occasionally noted

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