Branchial cleft cyst (cleft sinus)

A branchial cleft cyst is a birth defect found in the neck or just below the collarbone (clavicle) that may be visible as a pit in the skin, a projection of tissue, or a lump.

Causes, incidence, and risk factors 

Branchial cleft cysts appear early during development of the embryo when tissues of the branchial cleft (the area in the neck and collarbone) fail to develop normally. Open spaces called sinuses may remain on one or both sides of the neck.

A cyst may form from fluid drained from a sinus, and the cyst or sinus can become infected.


  • Small pits, lumps, or skin tags at either side of the neck or just below the collarbone  
  • Fluid drainage from a pit on the neck

Signs and tests 
Your baby’s health care provider will be able to diagnose this condition with a physical examination. Testing is usually not necessary.

Infected branchial cleft cysts or sinuses require antibiotic treatment. If there are persistent problems with drainage or infection, any cysts should be surgically removed.

Expectations (prognosis) 
Most branchial cleft remnants require no treatment. If surgery is required, results are usually good.


Infection of the cyst or sinus

Calling your health care provider 

Call for an appointment with your health care provider if you notice a small pit, cleft, or lump in the neck or upper shoulder of your infant, especially if fluid drains from this area.

Johns Hopkins patient information

Last revised: December 6, 2012
by Dave R. Roger, M.D.

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