Branchial cleft cyst: A cavity that is a remnant from embryologic development and is still present at birth in one side of the neck, just in front of the large angulated muscle on either side (the sternocleidomastoid muscle). The cyst may not be recognized until adolescence, when it enlarges its oval shape. Sometimes a branchial cleft cyst develops a sinus or drainage pathway to the surface of the skin, from which mucus can be expressed. Total surgical excision is the treatment of choice. Also known as branchial cyst.