Overview
Second branchial cleft anomaly (also known as second branchial cleft cyst, sinus, or fistula) is a congenital malformation arising from incomplete obliteration of the second branchial cleft (also called the second pharyngeal cleft) during embryonic development. These anomalies are the most common type of branchial cleft malformation, accounting for approximately 90-95% of all branchial anomalies. They primarily affect the head and neck region and may present as a cyst (a closed, fluid-filled sac), a sinus (a blind-ending tract opening to the skin surface), or a fistula (a complete tract connecting the skin surface to the pharynx, typically opening internally at the tonsillar fossa). Clinically, second branchial cleft anomalies typically present as a painless, smooth, fluctuant mass along the anterior border of the sternocleidomastoid muscle in the lateral neck, most commonly in the upper to middle third. A sinus or fistula may present as a small opening on the skin of the lower lateral neck from which mucoid fluid may drain. These anomalies are present from birth but may not become clinically apparent until childhood or even adulthood, often following an upper respiratory tract infection that causes the lesion to enlarge or become infected. When infected, the mass becomes tender, erythematous, and swollen, and may form an abscess. Treatment is primarily surgical, with complete surgical excision being the standard of care to prevent recurrent infections and potential complications. Surgery is ideally performed when the lesion is not actively infected. If infection is present, initial management includes antibiotics and, if necessary, incision and drainage, followed by definitive surgical excision once the acute inflammation has resolved. Recurrence rates after complete excision are low but increase if the anomaly has been previously infected or incompletely removed. There is no medical therapy that can resolve these anomalies without surgery.
Sporadic
Usually appears on its own, not inherited from a parent
Variable
Can begin at different ages, from infancy through adulthood
Treatments
No FDA-approved treatments are currently listed for Second branchial cleft anomaly.
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Specialists
View all specialists →No specialists are currently listed for Second branchial cleft anomaly.
Treatment Centers
8 centersBaylor College of Medicine Rare Disease Center ↗
Baylor College of Medicine
📍 Houston, TX
🏥 NORDStanford Medicine Rare Disease Center ↗
Stanford Medicine
📍 Stanford, CA
🔬 UDNNIH Clinical Center Undiagnosed Diseases Program ↗
National Institutes of Health
📍 Bethesda, MD
🔬 UDNUCLA UDN Clinical Site ↗
UCLA Health
📍 Los Angeles, CA
🔬 UDNBaylor College of Medicine UDN Clinical Site ↗
Baylor College of Medicine
📍 Houston, TX
🔬 UDNHarvard/MGH UDN Clinical Site ↗
Massachusetts General Hospital
📍 Boston, MA
🏥 NORDMayo Clinic Center for Individualized Medicine ↗
Mayo Clinic
📍 Rochester, MN
👤 Mayo Clinic Center for Individualized Medicine
🏥 NORDUCLA Rare Disease Day Program ↗
UCLA Health
📍 Los Angeles, CA
Travel Grants
No travel grants are currently matched to Second branchial cleft anomaly.
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Common questions about Second branchial cleft anomaly
What is Second branchial cleft anomaly?
Second branchial cleft anomaly (also known as second branchial cleft cyst, sinus, or fistula) is a congenital malformation arising from incomplete obliteration of the second branchial cleft (also called the second pharyngeal cleft) during embryonic development. These anomalies are the most common type of branchial cleft malformation, accounting for approximately 90-95% of all branchial anomalies. They primarily affect the head and neck region and may present as a cyst (a closed, fluid-filled sac), a sinus (a blind-ending tract opening to the skin surface), or a fistula (a complete tract connec
How is Second branchial cleft anomaly inherited?
Second branchial cleft anomaly follows a sporadic inheritance pattern. Genetic counseling can help families understand recurrence risk and testing options.